r/mdsimulation

These are the textbooks I used when I took the graduate class. They go through MD simulations in Fortran, but you can apply the authors' techniques in any language (I used python in the class). If you are also looking for a decent visualizer that is free, JMOL works great and all you need is a .xyz file output from your code to make it work.

(Monographs in Physical Chemistry) J. M. Haile - Molecular dynamics simulation_ elementary methods-Wiley-Interscience (1992)

(Computational science series 1) Daan Frenkel, Berend Smit - Understanding molecular simulation_ from algorithms to applications-Academic Press (2002)

Hello all,

I have recently started to work with GROMACS and I have some questions.

I have complete the Lyzome in water tutorial, however I am interested in simulation relatively more simple systems, such as a solution of 4-Cyano-4'-pentylbiphenyl. In this way, the first problem I had was how to obtain the PDB file.

To solve this problem, I generated it in the Avogadro software, however this created a problem, it assigns this RESID: UNL. In this way, I was not able to use the pdb2gmx since none of the force fields recognised this UNL. To circumvent this problem I tried to use PRODRG (which eliminates some hydrogen atoms and therefore it is not good), topolgen and MKTOP.

Since I wanted to

I'm looking for advice or a coauthor/collaborator with experience in molecular dynamics and computational biology.

My project is an LNP based on the general structure of Moderna-style LNPs, using a VHH nanobody targeting the adhesion-like protein MRU_1503 of Methanobrevibacter ruminantium. The LNP encapsulates 3-NOP and aspartate to minimize disruption of the rumen microbiome while still inhibiting methanogenesis. The design also includes PEI-R to help overcome the methanogen cell wall and provide access to the membrane.

I already have in silico binding data for the VHH ligand, including Gibbs free energy, affinity estimates, and evidence of up to six potential hydrogen bonds between the

I'm a beginner in the field of bioinformatics. I've experience in wet lab techniques, but Bioinformatics never before. This global pandemic has forced me to look into other fields of this discipline and Bioinformatics seem very promising and very confusing at the same time. Probably because I don't have anyone to guide me right now. I've seen some people doing some works in molecular dynamics and honestly I'm fascinated even without not understanding anything almost. Now I too want learn this skill and practice it myself. So far I've learnt that it's a very hardware intensive tool. I have an i5 9400F processor with rtx2060. Now my main concern is where do I begin the journey? What resources

Oh, gosh. Even MD group on REDDIT. Seems to be pretty dead now.

I found this group when looking for RTX2080 performance on MD.

But let's revive this sub and discuss MD software! There are a lot of MD programs and it is hard to choose starting point.

Let me start, I work in Maestro and thus prefer Desmond. Also, for my drug discovery project I want to learn Amber and AceMD for precise evaluation of compound binding capability. But want to listen other opinions.

P.S.: sorry for my english - non-native speaker

Hi all, Is there such a thing as online mentor? I mean, would it be possible to use some senior simulating-scientist as your helping guide online. It is possible to use the help of people face to face, but an online mentor would be the best when you want to ask anything stupid, or when you want to get just general studying guide. What do you suggest? Best

Hi, i'm Daniel, the founder of LIMA Dynamics. LIMA is a startup using MachineLearning to achieve superior simulation speeds. Our goal is to achieve simulations 14x faster than GROMACS at the >2,000,000 atoms scale.

We are currently looking for an innovative mind that can help us implement electrostatic forces, and validate the correctness of our simulations.

So if you are - or know someone - who has experience with molecular dynamics simulations, and brave enough to dive into the equations allowing such simulations to take place, then please reach out. Send me a DM or an email to [email protected]

You can read more about LIMA on our page here:

QUESTION: Is anyone aware of free sources for lammpstrj files? I am hoping to obtain one for a large box of water molecules at a variety of temperatures, with as many molecules included as possible.

For example, here's one of my files:

NSTEP = 50000 TIME(PS) = 350.000 TEMP(K) = 298.80 PRESS = 0.0

Etot = -100192.1518 EKtot = 24511.8379 EPtot = -124703.9897

BOND = 1553.3334 ANGLE = 3854.6417 DIHED = 5980.5163

1-4 NB = 1745.0203 1-4 EEL = 12980.5904 VDWAALS = 10964.6537

EELEC = -161782.7456 EHBOND = 0.0000 RESTRAINT = 0.0000

------------------------------------------------------------------------------

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wrapping first mol.: -79.54229 0.00000 0.00000

wrapping first mol.: -79.54229 0.00000 0.00000

wrapping first mol.: -79.54

Hi everyone, I have setup with Ryzen 2990WX and Gigabyte RTX 2080 Ti. I've tried running Desmond simulations on it. It runs fine but I'm afraid I will ruin the GPU as it is running at 71°C, about 80% fan speed, 300 W / 300 W capacity, 86 % GPU utility. An average run will take about 12 hours. Do you think it's safe to run it this way? Have you had any experience with this type of setup? Many thanks!

I am confused by the output of the iRED. On the paper about it, they mention this the iRED cpptraj analysis will get you the eigenmode collectivity value and the eigenvalue. I can not get my ahead around where this value is.

Hello,
I want to perform a MD simulation of diffusion of a liquid in water, but I am a newbie in this domain (although I'm familiar with computers and Linux). I found some documentation about Tinker, is this software good for my needs?

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Thanks for your help!