Re: [gmx-users] Setting a electric field in a simulation

Dear Prof. David van der Spoel, Thank you very much for your helpful response. I am sorry for further asking. I tried to field information during the MD using -field option. It gave me * @title "Applied electric field" @xaxis label "Time (ps)" @yaxis label

Re: [gmx-users] pressure fluctuation and actual density

Some examples of the pressure fluctuations that you can get can be seen here: https://twitter.com/dr_dbw/status/968624615063937025 Pressure is a macroscopic property. The smaller the system, the larger the fluctuations will be. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics

Re: [gmx-users] checkpoint files with replica exchange/ -multidir

Thanks Mark, >From my experience so far if I stayed at 4ps, I would continue to get lower exchange rates. As for starting at 1ps, my system must not have been equilibrated because it was blowing up on the first exchange attempt which Is why I decided to restart with the checkpoint file. Dan On

Re: [gmx-users] checkpoint files with replica exchange/ -multidir

Hi, On Thu, 12 Mar 2020 at 20:39, Daniel Burns wrote: > Hello, > > I'm using 2 replicas to test exchange conditions. I restarted a run and > included the checkpoint file name (which is identical in each directory > provided under the -multidir option). After the restart, I'm getting 100% > exc

[gmx-users] checkpoint files with replica exchange/ -multidir

Hello, I'm using 2 replicas to test exchange conditions. I restarted a run and included the checkpoint file name (which is identical in each directory provided under the -multidir option). After the restart, I'm getting 100% exchange when before it was 50%. Does the -cpi option work properly fo

Re: [gmx-users] Parametrization of Mn(ii) in charmm force field

On 3/12/20 5:15 AM, Alessandra Villa wrote: Hi, You have to search in literature for parameters for Mn ions compatible with CHARMM36 and with the water model (some ions are parameterized to reproduce structural, thermodynamics, kinetic properties in water solution). For example Mn non-bond

[gmx-users] pressure fluctuation and actual density

 hiI want to simulate a box of methyldiethanol amine and see the  actual density . I set 100 amine molecules in a cubic box 4×4×4 (nm^3)I first used energy minimization for 400ps . then I used npt for 2ns. I saw a lot fluctuation in pressure .pressure is 1bar.I used Rahman barostat. is my p

[gmx-users] (no subject)

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Re: [gmx-users] GROMACS automation

> The paper information is as below : > Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic > Light-Emitting Diode Films > Authors: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J. > Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R. > Gentle,

Re: [gmx-users] GROMACS automation

The paper information is as below : Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic Light-Emitting Diode Films Authors: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mar

Re: [gmx-users] GROMACS automation

> I was planning to put the velocities in the .gro file from which I am > inserting the molecules. If the gmx insert-molecules will ignore the > velocities of the atoms, can you please guide me how can I insert the > molecules with a velocity ? > I have read a paper which mentions that they inserte

Re: [gmx-users] slurm and gromacs

This link should help: http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts - John > Dear gromacs users > > I am doing md simulation of protein in a cluster system with > Slurm Workload Manager using following job file: >

[gmx-users] slurm and gromacs

Dear gromacs users I am doing md simulation of protein in a cluster system with Slurm Workload Manager using following job file: --- #! /bin/bash #SBATCH --job-name Pr_lig #SBATCH -n 28 #SBATCH --time 300:30:00 #SBATCH --mem 5

Re: [gmx-users] GROMACS automation

I was planning to put the velocities in the .gro file from which I am inserting the molecules. If the gmx insert-molecules will ignore the velocities of the atoms, can you please guide me how can I insert the molecules with a velocity ? I have read a paper which mentions that they inserted the mole

[gmx-users] Vacuum simulations with Gromacs 2018

Dear all, I want to do vacuum simulations for calculating partition coefficients. I found the appropriate options for gromacs 5 through one of the previous threads. cutoff-scheme = group ns_type= grid rlist = 0 nstlist= 0 vdwtype= cutoff

Re: [gmx-users] Nose-Hoover vs Berendsen vs V-rescale

Hi, It's very likely a good idea to get the velocity distribution right, for the situation you're trying to model. Check out https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0 (and the other great LiveComsJ material!) Mark On Thu, 12

Re: [gmx-users] Parametrization of Mn(ii) in charmm force field

Hi, You have to search in literature for parameters for Mn ions compatible with CHARMM36 and with the water model (some ions are parameterized to reproduce structural, thermodynamics, kinetic properties in water solution). For example Mn non-bonded parameters can be found *J. Phys. Chem. A* 200