Re: [gmx-users] Details of g_rdf functions in version 4.6.5.

Dear Warren, So if I understand you correctly, does this mean that the g_rdf default settings function starts off with taking my Ethyl Acetate's first atom assigned in *.tpr, then selects Ethanol's first atom and calculates the RDF for this interaction. Now followed by Ethanol's second atom,

[gmx-users] cgenff generated force field problem

Hi Gromacs Users, I am trying to do a protein-ligand simulation where the force field of the ligand has been generated by cgenff. I have manually edited the protein .top file, which has been generated by pdb2gmx, by adding the lines #include .prm and #include .itp at appropriate positions.

[gmx-users] Cgenff generated force field issue

Hi Gromacs Users, I am trying to do a protein-ligand simulation where the force field of the ligand has been generated by cgenff. I have manually edited the protein .top file, which has been generated by pdb2gmx, by adding the lines #include .prm and #include .itp at appropriate positions.

[gmx-users] Cgenff generated force field problem

Hi Gromacs Users, I am trying to do a protein-ligand simulation where the force field of the ligand has been generated by cgenff. I have manually edited the protein .top file, which has been generated by pdb2gmx, by adding the lines #include .prm and #include .itp at appropriate positions.

Re: [gmx-users] How to measure distance and find salt bridges in GROMACS ?

Good page to have a thorough read of is http://manual.gromacs.org/documentation/current/user-guide/cmdline.html http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html http://manual.gromacs.org/documentation/current/onlinehelp/gmx-saltbr.html Try some things, see what you

[gmx-users] Improving the MD simulations.

Hi There, I am new for MD simulations using gromacs and I would like to enhance my MD simulations time run on the servers. I execute the following command: gmx mdrun -nt 24 -s full.tpr -e full1.edr -o full1.trr -c p4iw_full1.gro -g flog1.log For 100 ps it took about 1 hr (as I can see from the

Re: [gmx-users] Details of g_rdf functions in version 4.6.5.

The selection you made means you calculated the RDF of all ethyl acetate atoms to all ethanol atoms. The atoms it uses are those in each of the index groups you selected. The 0.2nm start of the function is reasonable as that is how close the center of two atoms can get. What you want to use is

[gmx-users] How to measure distance and find salt bridges in GROMACS ?

Hi all, I want to measure distance between two specific residues during molecular dynamics in GROMACS. I am not aware of gmx distance command for distance calculations. Second, I would like to know how to find the salt bridges during the period of molecular simulation. Thank you in advance.

Re: [gmx-users] cmap error while making tpr file from dcd file

Hi, XTC files don't have CMAP and grompp doesn't accept them as the main input. How exactly are you calling grompp to get such an error? The problem is likely related to the .top file. Mark On Thu., 13 Jun. 2019, 18:10 Santanu Santra, wrote: > hey users, > While I'm trying to

Re: [gmx-users] GPU issue - system that was stable on CPUs crashes

Hi, Thanks for your suggestions! I looked at the box volume over time in the CPU-only NPT run, and the volume doesn’t change a lot: 0.00 523.472656 nm^3 1.00 520.086731 2.00 520.337769 3.00 518.600708 ... 100.00 521.340820 I used Parrinello-Rahmen as barostat (on CPU and

Re: [gmx-users] Grompp not producing tpr files

A segmentation fault is a “crash” not a normal exit. The only information you have there is where the program got to before it crashed. No log file? Peter Sent from my iPhone > On Jun 13, 2019, at 6:04 PM, Israel Estrada wrote: > > Thanks for the replies! > > Mark, the process seemed to

[gmx-users] cmap error while making tpr file from dcd file

hey users, While I'm trying to calculate some properties in gromacs from dcd files (NAMD), I followed the protocol in generating xtc file from vmd by loading psf and pdb files, and by grompp engine using a similar mdp file equivalent to my NAMD configuration file, I got CMAP error

Re: [gmx-users] Grompp not producing tpr files

Hello, Yes, the last part indicates an error that should not happen. Which version did you use to run this? If it is a version before 2018, can you try the newer versions to see if the error persists? Cheers Paul On Thu, 13 Jun 2019, 17:04 Israel Estrada, wrote: > Thanks for the replies!

Re: [gmx-users] Grompp not producing tpr files

Thanks for the replies! Mark, the process seemed to "finish" properly (my terminal did not close, and the command line was waiting for the next command as if it ran normally). I looked for the output file (ions.tpr) in the working directory, or any new files, but nothing was generated.

Re: [gmx-users] simulation continuation - gen-vel = yes

Thank you, Mark. That makes me feel better. - John > Hi, > > gen-vel is interpreted by grompp, never mdrun. > > Mark > > On Thu., 13 Jun. 2019, 13:04 John Whittaker, < > johnwhitt...@zedat.fu-berlin.de> wrote: > >> Hi all, >> >> I have a simple question that I hope someone can answer. >> >> When

Re: [gmx-users] simulation continuation - gen-vel = yes

Hi, gen-vel is interpreted by grompp, never mdrun. Mark On Thu., 13 Jun. 2019, 13:04 John Whittaker, < johnwhitt...@zedat.fu-berlin.de> wrote: > Hi all, > > I have a simple question that I hope someone can answer. > > When I began my simulation, my .mdp file had "gen-vel = yes" in order to >

[gmx-users] simulation continuation - gen-vel = yes

Hi all, I have a simple question that I hope someone can answer. When I began my simulation, my .mdp file had "gen-vel = yes" in order to generate some initial velocities. My next simulation was a continuation of the first (I am setting nsteps = -1 and running mdrun with the flag -maxh in order

Re: [gmx-users] Some suggestions about the gmx current tool

Hi Mark, Thank you for your reply! I opened a new issue with this information in the link you mentioned. Best regards, Mahsa On Wed, Jun 12, 2019 at 10:26 PM Mark Abraham wrote: > Hi Mahsa, > > Thanks very much for your feedback. Those look like useful changes to the > code. Can you please

[gmx-users] Details of g_rdf functions in version 4.6.5.

From: Henry Vider Sent: Thursday, June 13, 2019 11:37 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Details of g_rdf functions in version 4.6.5. Dear GROMACS mailing list, I am writing here due to the inconsistencies in my Radial Distribution Functions (RDF) calculations. Currently I