[gmx-users] gmx make_ndx - separating pulling groups by fragments

Hello! I'm trying to conduct a pulling simulation with two identical proteins and centers of mass distance being the reaction coordinate. They are distinguished by fragment index in vmd (0 and 1), but the residues in the .gro file run from 1 to 178 and again from 1 to 178. How to I used

[gmx-users] Restart after crash

I had restarted my crash run after around 271 ps. The simulation ran fine after that and showed *starting mdrun 'Protein in water'250 steps, 5000.0 ps (continuing from step 135600,271.2 ps).step 2499900, remaining wall clock time: 1 s Writing final coordinates.step

[gmx-users] Command question

Hi, I am trying to use editconf command to modify my system, but I got an error massage :"-bash editconf command not found". I tried "gmx editconf", the error shows that "-bash gmx command not found". I am using gromacs 4.5.5 on westgrid (orcinus). I wonder does anyone have any experience

Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue

Hi, you could have a look into http://www.hecbiosim.ac.uk/fesetup to set up your system. It is late evening here so I will answer in more detail tomorrow. Cheers, Hannes. On Mon, 3 Oct 2016 19:57:07 + Guanglin Kuang wrote: > Dear Gromacs users, > > Has any of you

[gmx-users] ion parameters in amber99sb

Hi, I was wondering, where do the Lennard Jones parameters for ions come from in the amber99sb force fields ported in gromacs? Best, Irem -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue

I am sorry the attachments cannot be seen. The attachments are now available through this Google Drive link: https://drive.google.com/open?id=0B8f0-zVoaBXNZUpuM2ttNWQ1QUE Best regards! Guanglin -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] Gromacs Relative Free Energy Calculation Issue

Hi, The list cannot accept attachments, so if you would like to share files, please do so via a file-sharing service, and post the links you wish to share :-) Mark On Mon, Oct 3, 2016 at 9:57 PM Guanglin Kuang wrote: > Dear Gromacs users, > > Has any of you managed to use

[gmx-users] Gromacs Relative Free Energy Calculation Issue

Dear Gromacs users, Has any of you managed to use Gromacs to do relative free energy calculations? I have some technical questions that would need your suggestions. I am trying to reproduce the Amber free energy calculation using PMEMD

[gmx-users] problem with gmx energy

Dear Gromacs users one of the output of gmx energy is Pressure x-x , but its value is for the whole system, so does exist anyway to get pressure x-x for one special group of the system? for example, my system contains 2 group as DOPC and Sol and I want to elicit pressure x-x for DOPC. Thanks

[gmx-users] problem with gmx energy

Dear Gromacs users one of the output of gmx energy is Pressure x-x , but its value is for the whole system, so does exist anyway to get pressure x-x for one special group of the system? for example, my system contains 2 group as DOPC and Sol and I want to elicit pressure x-x for DOPC. Thanks

Re: [gmx-users] Point charges?

On 10/3/16 1:10 PM, Marko S wrote: Hello everyone. Thanks for the software and hopefully for your help on advance. I'm a bit confused, since I can't find the answer in the manual. But where are the atom point charges written in which Gromacs output file? I need that data for further analysis

[gmx-users] Point charges?

Hello everyone. Thanks for the software and hopefully for your help on advance. I'm a bit confused, since I can't find the answer in the manual. But where are the atom point charges written in which Gromacs output file? I need that data for further analysis of my system. Thanks! -- Gromacs

[gmx-users] Errors in building gromacs 5.0.4 MPI version

I got the following errors when I tried to install gromacs MPI version 5.0.4 on a Fedora 18 I wrote on the command line the following: cmake '/home/steve/Downloads/gromacs-5.0.4'-DGMX_BUILD_FFTW=ON -DGMX_MPI=ON  SCREEN PRINT OUT: -- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so  -- Could NOT

[gmx-users] Protein Membrane SImulation using CHARMM 36 forcefield

I want to perform membrane protein simulation similar to justin's KALP tutorial, but using charmm 36 forcefield instead. I will be using POPC model membrane, the charmm36 based coordinates for which can be found in http://terpconnect.umd.edu/~jbklauda/research/download.html But, I am not sure if

Re: [gmx-users] Protein Membrane SImulation using CHARMM 36 forcefield

On 10/3/16 10:43 AM, Roshan Shrestha wrote: I want to perform membrane protein simulation similar to justin's KALP tutorial, but using charmm 36 forcefield instead. I will be using POPC model membrane, the charmm36 based coordinates for which can be found in

Re: [gmx-users] segmentation fault in md

On 10/3/16 2:38 AM, ISHRAT JAHAN wrote: Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am pasting my em.mdp and pr.mdp file below- em.mdp ; ;User spoel (236) ;Wed Nov 3

Re: [gmx-users] moleculaes breaking off after EM - help

On 10/2/16 10:09 PM, Thejus Kartha wrote: Greetings! I was performing an EM run with an array of dioxane molecules, for which I had produced co-ordinates from PRODRG. I got the co-ordinates, and made an array of it, using the gmx genconf module, and corrected my topology file. Then, I

Re: [gmx-users] energy minimisation - LINCS WARNING

That’s a good suggestion, Mark. Will do :-) Thanks Anthony Dr Anthony Nash Department of Chemistry University College London Skeletal Tissue Dynamics Group Committee member of London Matrix Group @LondonMatrixGrp On 03/10/2016 12:03, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

Re: [gmx-users] energy minimisation - LINCS WARNING

Hi, Sounds like you could check the output from that tool, and if it gave no warning (or offers you no way to choose another rotamer) then you could make some constructive feedback to its authors :-) Mark On Mon, 3 Oct 2016 11:22 Nash, Anthony wrote: > > Hi Justin, > > >

Re: [gmx-users] energy minimisation - LINCS WARNING

Hi Justin, I’ve tried out all of your suggestions, they worked to an extent but the in vacu idea was a good call as it’s actually helped me isolate what the real problem is: I-TASSER has put the C-N backbone bond of two residues through the ring of an adjacent PHE residue! Thanks Anthony On

Re: [gmx-users] g_membed failure

Hi Mark, Yes I started with the tutorial you mentioned. From which I understood I need some kind of embed.dat file and that my .mdp file has to have this part: integrator = md energygrps = Protein_Lig (since I have a ligand and I have grouped it with the protein using an index file)

Re: [gmx-users] mail about installation og gromacs 4.6.1

Hi, If you feel you must install software that is three years old and no longer supported, please at least get the latest bug-fix version of it (4.6.7). You should consider carefully one of the more recent, faster and less buggy versions. I can't tell what your problem is, but my guess is that

[gmx-users] segmentation fault in md

Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am pasting my em.mdp and pr.mdp file below- em.mdp ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp

Re: [gmx-users] restarting the crashed run

Hi, The default name for that file is confout.gro, which it will be unless you chose a different name with gmx mdrun -c nvt.gro or gmx mdrun -deffnm nvt However, you can sometimes get slightly better results by using gmx grompp -c whatever -p topol -t nvt.cpt -f npt -o npt because now the

Re: [gmx-users] gromacs mdrun problem

Hi, The list does not accept attachments, unfortunately. However, your problem is probably solvable via the advice at http://www.gromacs.org/Documentation/Terminology/Blowing_Up. There's also probably no reason to do a run with position restraints for urea in water, since there's little that is

[gmx-users] gromacs mdrun problem

Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am attaching my em.mdp and pr.mdp file below- Thanks in advance -- Gromacs Users mailing list * Please search the archive at