[gmx-users] nonbonded molecules and atoms

  Dear all, I am new to gromacs software. I was trying to make simple sodium nitrate (NaNO3) molecules. I have made .pdb file. then I got .gro file from pdb2gmx. But, I got struck in .itp file. Please help me. ( Na is nonbonded to any of N and O in NaNO3. And Na is also nonbonded to Na of 2nd Na

Re: [gmx-users] fatal error invalid pairs 5

On 10/6/16 3:20 PM, Devon Dillon wrote: this is my error message -- Program gmx, VERSION 5.0.2 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-5.0.2/src/gromacs/gmxpreprocess/topdirs.c, line: 166 Fatal error: Invalid pairs type 5 For m

Re: [gmx-users] Gromacs GMX_BUILD_FFTW warning in building Gromas 5.0.4

On 10/6/16 1:34 PM, Steve Seibold wrote: HelloI have been attempting to compile and build Gromacs 5.0.4for a couple of weeks. I have been following the instructions (having also readGromacs 5.0 instruction in Manual..) at https://ourphysics.org/wiki/index.php/How_to_compile_Gromacs#Gromacs_5.1

[gmx-users] fatal error invalid pairs 5

this is my error message -- Program gmx, VERSION 5.0.2 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-5.0.2/src/gromacs/gmxpreprocess/topdirs.c, line: 166 Fatal error: Invalid pairs type 5 For more information and tips for troubleshooting

Re: [gmx-users] high-temperature MD

Depends, actually. There are reasons one might want to simulate a system at 380 K in NVT using the average box volume from the 300 K NPT simulation. Temperature replica exchange typically employs NVT and so might other temperature-based enhanced sampling approaches. Justin's right, you have to

Re: [gmx-users] g_spatial Problem

This works for me (careful with line wrapping if this email or the list mangles it): #!/bin/bash PATH=/project2/p/pomes/cneale/GPC/exe/intel/gromacs-4.6.7/exec/bin:$PATH export GMXLIB=/project2/p/pomes/cneale/GPC/exe/intel/gromacs-4.6.7/exec/share/gromacs/top # setup variables CENTRAL="CHO" SD

[gmx-users] Gromacs GMX_BUILD_FFTW warning in building Gromas 5.0.4

HelloI have been attempting to compile and build Gromacs 5.0.4for a couple of weeks. I have been following the instructions (having also readGromacs 5.0 instruction in Manual..) at https://ourphysics.org/wiki/index.php/How_to_compile_Gromacs#Gromacs_5.1.1_MPI.2C_single  Specifically, I have use

Re: [gmx-users] mdrun don't write a checkpoint file

Thank You Justin I run a short equilibration on my system and now I get the checkpoint file. Simon Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Justin Lemkul Gesendet: Donnerstag, 6. Oktober 2016 15:33 An: gmx-us...@gromacs.org

Re: [gmx-users] mail regarding installation of geomacs5.1.2

On 10/6/16 9:13 AM, subramanian vidhyasankar wrote: Dear mark and justin sir Thank you for your previous reply I installed successfully the gromacs5.1.2 But my bin directory does not contain any executable files *it contains tool gmx_d only* When i run

Re: [gmx-users] high-temperature MD

On 10/6/16 8:54 AM, OuyangYanhua wrote: Dear Justin, I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare with the 300K-MD. The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So I want to know the high-temperature(380K) MD should run the s

Re: [gmx-users] mdrun don't write a checkpoint file

On 10/6/16 8:23 AM, Menig, Simon wrote: Thank you for your fast answer Justin I looked up the log files but I found no error and my disc space is sufficient and the simulation seem to end normal. Could the Problem be that my Simulation time is shorter than 15 min (max 5000 steps) ? (Shouldn'

[gmx-users] mail regarding installation of geomacs5.1.2

Dear mark and justin sir Thank you for your previous reply I installed successfully the gromacs5.1.2 But my bin directory does not contain any executable files *it contains tool gmx_d only* When i run the following command *./gmx_d g_select_d -h* i got

Re: [gmx-users] high-temperature MD

Dear Justin, > I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare with the 300K-MD. The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So I want to know the high-temperature(380K) MD should run the same as the 300k, which means the 380k is al

Re: [gmx-users] mdrun don't write a checkpoint file

Thank you for your fast answer Justin I looked up the log files but I found no error and my disc space is sufficient and the simulation seem to end normal. Could the Problem be that my Simulation time is shorter than 15 min (max 5000 steps) ? (Shouldn't it write a cpt file after the End of the

Re: [gmx-users] mdrun don't write a checkpoint file

On 10/6/16 7:41 AM, Menig, Simon wrote: Hi, I am new to GROMACS and I wanted to run a Coars-Grain simulation but gmx mdrun doesn't write a checkpoint file and I found no solution for my Problem in the Docs or Internet. I hope someone can help me with this problem, I need this files for ext

Re: [gmx-users] Different Results with Different Platforms

Thank you very much, Justin. I was take note of this in subsequent runs. Thank you so, so much for your assistance. It is greatly appreciated! -- Best wishes, Kelechi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List bef

[gmx-users] mdrun don't write a checkpoint file

Hi, I am new to GROMACS and I wanted to run a Coars-Grain simulation but gmx mdrun doesn't write a checkpoint file and I found no solution for my Problem in the Docs or Internet. I hope someone can help me with this problem, I need this files for extending my Simulation (similar to Lysozyme tu

Re: [gmx-users] Fatal error Invalid pairs 5

On 10/5/16 11:26 PM, Devon wrote: I'm having big problems. I generated a topology using atb. I'm using the external force fields recommended. I'm getting an invalid pairs 5 error. It would be greatly appreciated if someone could help alleviate some stress. Thank you Please provide a full

Re: [gmx-users] high-temperature MD

On 10/6/16 3:52 AM, YanhuaOuyang wrote: Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As we know, the MD is equilibrated firstly at NVT, then at NPT ensemble and production MD at NPT ensemble normally. Does someone know whether the 380K-MD can only perform at NVT e

Re: [gmx-users] Different Results with Different Platforms

On 10/6/16 7:13 AM, Kelechi Okoroafor wrote: Thank you for the tip, Justin. I incorrectly thought that the coordinates and box dimensions were sufficient to preserve the pressure of the system. I shall make a habit of restarting simulations with the checkpoint file rather than .gro files. My s

Re: [gmx-users] Different Results with Different Platforms

Thank you for the tip, Justin. I incorrectly thought that the coordinates and box dimensions were sufficient to preserve the pressure of the system. I shall make a habit of restarting simulations with the checkpoint file rather than .gro files. My sequence of commands were: - gmx grompp -f

[gmx-users] PMF of a short peptide on a solid surface

Dear gromacs user, In order to simulate the PMF of a adsorbed short peptide on a solid surface, first I minimised and equlibrated(NVT and NPT) the system and then I did a 60 ns of production run in which the peptide fully adsorbed to the surface. I used these out put to pull away the peptide from

Re: [gmx-users] Replica Exchange MD

Thank you very much for your reply and suggestions. I am discussing with system admin regarding this issue. With Best Regards, Kalyanashis Jana On Wed, Oct 5, 2016 at 6:01 PM, Mark Abraham wrote: > Hi, > > On Wed, Oct 5, 2016 at 2:17 PM Kalyanashis Jana > wrote: > > > Hi Mark, > > The MD run s

[gmx-users] high-temperature MD

Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As we know, the MD is equilibrated firstly at NVT, then at NPT ensemble and production MD at NPT ensemble normally. Does someone know whether the 380K-MD can only perform at NVT ensemble since the temperature(380K) is a