[gmx-users] atomselection for index group of cyclic rings

Dear all, I am interested in measuring the distance between two cyclic rings present in the residues and ligands over time. Can you kindly suggest how to go about this? Specially, if i am interested in measuring the distance between the center of the two rings over time. Thank you -- Regards,

[gmx-users] RIN (Residue interaction network) for protein ligand interactions

Dear All, I am interested in viewing the Residue Interaction network during a protein - ligand simulation. Can someone suggest an easy way to go about it? I tried to use gRINN tool but I guess it doesn't work if ligands are present. Thanks in advance. -- Regards, Prasanth. -- Gromacs Users

Re: [gmx-users] How to solve the "LINCS WARNING" problem

Thank you Yu Du I encountered the problem while I have tried to simulate the protein-ligand complex system. 1. I generated the all atom ligand topology file from the ATB website. And I make both ligand .gro file and protein .gro file by using pdb2gmx and editconf module. 2. Then I run

Re: [gmx-users] Velocities from the .gro file

Sent from my iPhone > On Apr 16, 2020, at 7:53 PM, Mohamed Abdelaal wrote: > > I have one more question please regarding the velocity. No problem. > > What is the mean value for the velocity being generated by GROMACS ? Is it > zero ? Yes. > > I have also understood fr om the below

[gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation

Dear all, A ligand molecule (lig) contains a Chlorine atom in it. While attempting to performing a protein-ligand simulation, the Gromacs returns an error message. It is observed that the *CGenFF server * Generate two additional lines, as shown below, in lig.str file ATOM LP1LPH 0.050 !

Re: [gmx-users] Velocities from the .gro file

I have one more question please regarding the velocity. What is the mean value for the velocity being generated by GROMACS ? Is it zero ? I have also understood fr om the below paragraph which is written in the manual section 3.4.1, that the values generated are selected from the range between 0

Re: [gmx-users] Question on running gmx trjconv without 2 prompts

Thank you Dr. Lemkul, these two websites are very helpful. Thanks! On Thu, Apr 16, 2020 at 8:17 PM Justin Lemkul wrote: > > > On 4/16/20 8:12 PM, Lei Qian wrote: > > Dear users, > > > > Could I ask: how to run gmx trjconv without 2 prompts? > > I select 'Protein' to center, and 'System' to

[gmx-users] Failed to find GROMACS magic number in trr frame header

Dear GMX users, Hello, I performed MD simulation using gromacs 2018.7v. During this simulation, the calculation was stopped because of the electric cut. Then, I continued the simulation using "gmx mdrun with -noappend" in order to get separate trajectory for the safety of data. After that, I

Re: [gmx-users] Measuring bond distances, angles and dihedrals

Hi Robert, I have only used MDTraj for distance calculation between trajectories, no experience in parameters extraction. If MDTraj cannot satisfy your custom requirement, that I recommend VMD Tcl scripts to extract related information. It probably takes you a week to master the VMD system,

Re: [gmx-users] Question on running gmx trjconv without 2 prompts

On 4/16/20 8:12 PM, Lei Qian wrote: Dear users, Could I ask: how to run gmx trjconv without 2 prompts? I select 'Protein' to center, and 'System' to output. I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do

[gmx-users] Question on running gmx trjconv without 2 prompts

Dear users, Could I ask: how to run gmx trjconv without 2 prompts? I select 'Protein' to center, and 'System' to output. I put indexes of 'Protein' and 'System' into 1 .ndx file, add -n Protein_System.ndx to gmx trjconv command, however, Gromacs cannot do the selection automatically and asked me

Re: [gmx-users] about problem running script for Gibbs free energy simulation

Ah let me fix that and try again. I will let you know how it goes. Thank you very much for all the help On Thu, Apr 16, 2020 at 4:23 PM Justin Lemkul wrote: > > > On 4/16/20 3:20 PM, lazaro monteserin wrote: > > But how do I declare this in the script? > > > > I have try for example: > > > >

Re: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"

Thank you for your reply, Alan. I didn't realize that I need to use thread-MPI in order to use the GPU communication features. Best regards, Leandro --- Leandro Oliveira Bortot Postdoctoral Fellow https://www.linkedin.com/in/leandro-obt/ Laboratory of Computational

Re: [gmx-users] about problem running script for Gibbs free energy simulation

On 4/16/20 3:20 PM, lazaro monteserin wrote: But how do I declare this in the script? I have try for example: FREE_ENERGY="/home/Lazaro/tutorial_gromacs" and then MPD="/$FREE_ENERGY/mpd" Using the " " But stills it doesn't work. I have all my .mdp files stored in a directory called "mdp"

Re: [gmx-users] about problem running script for Gibbs free energy simulation

But how do I declare this in the script? I have try for example: FREE_ENERGY="/home/Lazaro/tutorial_gromacs" and then MPD="/$FREE_ENERGY/mpd" Using the " " But stills it doesn't work. I have all my .mdp files stored in a directory called "mdp" inside the directory "tutorial_gromacs". Am I

Re: [gmx-users] about problem running script for Gibbs free energy simulation

On 4/16/20 1:47 PM, lazaro monteserin wrote: Dear Lemkul Thank you very much for the recommendation. I tried each step but separate and you were right I was missing the .gro in my directory. Now the script should work. But I am still unsure of how to declare the location of my file in the

Re: [gmx-users] about problem running script for Gibbs free energy simulation

Dear Lemkul Thank you very much for the recommendation. I tried each step but separate and you were right I was missing the .gro in my directory. Now the script should work. But I am still unsure of how to declare the location of my file in the environmental variable $FREE_ENERGY and $MDP. Do

Re: [gmx-users] Measuring bond distances, angles and dihedrals

Hi, I've carried out a number of equilibrations and I now want to extract bond distances, bond angles and dihedrals from the resulting trajectories. I'm using MDTraj to do this, which is working perfectly fine, however I'm not too happy with the results as they are not exactly how I want

Re: [gmx-users] about problem running script for Gibbs free energy simulation

On 4/16/20 11:48 AM, lazaro monteserin wrote: Dear Gromacs users, I have been trying to do the tutorial title: "Free Energy Calculations: Methane in Water" by Dr. Justin A. Lemkul but when I try to actualize my paths to the variables $FREE_ENERGY AND $MDP in the script *job.sh* I have

[gmx-users] about problem running script for Gibbs free energy simulation

Dear Gromacs users, I have been trying to do the tutorial title: "Free Energy Calculations: Methane in Water" by Dr. Justin A. Lemkul but when I try to actualize my paths to the variables $FREE_ENERGY AND $MDP in the script *job.sh* I have problems and I get the following error: Program: gmx

Re: [gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution

On 4/16/20 10:26 AM, Adarsh V. K. wrote: Dear all, While performing a protein ligand simulation, I received the following 'WARNING' message. How to manage this issue? just with ' -maxwarn 1 ' or any other method?

[gmx-users] WARNING 1 [file topol.top, line 60334] - How to manage? -maxwarn 1 or any other solution

Dear all, While performing a protein ligand simulation, I received the following 'WARNING' message. How to manage this issue? just with ' -maxwarn 1 ' or any other method? --- gmx grompp -f

Re: [gmx-users] How to solve the "LINCS WARNING" problem

If you haven't solved your LINCS WARNING, you need to show more details of how you got that problem, including the generation of your ligand topology file. There are maybe some errors in your ligand topology that you didn't figure out. Cheers, Yu From:

Re: [gmx-users] GROMACS PBS GPU JOB submission

Hi Tuanan, I think your problem can be separated into several parts: First, use one PBS script contains 4 GMX commands, shown as follows, may solve your problems: #PBS -l select=1:ncpus=40:mpiprocs=40:ompthreads=1:ngpus=1 mpirun -machinefile $PBS_NODEFILE -np 40 gmx_mpi mdrun -s nvt-prod1.tpr

Re: [gmx-users] How to solve the "LINCS WARNING" problem

Thank you for reply Du, You You said that "If you want more suggestion, you need to provide some details of the generation of ligand's topology” Du you mean that I modify my topology file manually?? > 2020. 4. 14. 오후 5:08, Yu Du 작성: > > Hi Jinyoung, > > I guess that the LINCS WARNING you

Re: [gmx-users] Multi-GPU optimization, "DD without halo exchange is not supported"

Hi Leandro, I see from your command line that you are using an external MPI library and running gmx_mpi via mpirun. The new GPU communication features are currently only supported with use of thread MPI (see

[gmx-users] GROMACS PBS GPU JOB submission

Hi everyone I am using GROMACS 2018 in a node with 80 core and 4 TESLA V1, the queue system is PBS. I am having some issues with the GPU selection, what I want is to use 1 GPU per job but GROMACS is always using all the four GPUs. My submission script is the following: #PBS -l

Re: [gmx-users] Problem force constant bond stretc.

Thanks a lot. Best regards, Paolo Il giorno gio 16 apr 2020 alle ore 07:57 David van der Spoel < sp...@xray.bmc.uu.se> ha scritto: > Den 2020-04-15 kl. 23:48, skrev Paolo Costa: > > Dear Gromacs users, > > > > I have a problem regarding force constant for bond stretching. By > employing > >

Re: [gmx-users] Trouble with restrained dihedrals

Den 2020-04-16 kl. 08:56, skrev Marko Petrovic: Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept

Re: [gmx-users] Trouble with restrained dihedrals

Bottom post: On 16 Apr 2020, at 08:56, Marko Petrovic mailto:ma...@kth.se>> wrote: Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or

[gmx-users] Trouble with restrained dihedrals

Hello I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for