Re: [gmx-users] MMPBSA analysis on GROMACS trajectory

Hi They have a web site and all of things you need is there: http://rashmikumari.github.io/g_mmpbsa/ On Mar 27, 2017 10:15 AM, "Neha Gupta" wrote: > Hi gromacs users, > > How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool of > amber software

Re: [gmx-users] Installing DSSP

Hi follow these steps: 1)sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.2.1-linux-i386 -O /usr/local/bin/dssp 2)sudo chmod a+x /usr/local/bin/dssp 3)export DSSP=/usr/local/bin/dssp On Fri, Feb 3, 2017 at 3:15 PM, Mark Abraham wrote: > Hi, > > On Fri, Feb

[gmx-users] DSSP Erorr

Hi to all first i run 'gmx do_dssp -s md.tpr -f md.xtc' i go this error: Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) then i put dssp executable file in the path 'usr/local/bin/dssp' and run following command : 'export DSSP=/usr/local/bin/dssp' now when i

[gmx-users] DSSP Error

Hi to all first i run 'gmx do_dssp -s md.tpr -f md.xtc' i go this error: Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) then i put dssp executable file in the path 'usr/local/bin/dssp' and run following command : 'export DSSP=/usr/local/bin/dssp' now when i

Re: [gmx-users] Error in energy groups

tnx Dr.Lemkul yes the problem was in the tc-grps. tc-grps= Protein Non-Protein and there is no Non-Protein group in index file. it's true that i use System for tc-grps? On Sun, Jul 24, 2016 at 11:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/24/16 3:17 PM,

[gmx-users] Error in energy groups

Hi all i have a protein with six chain. i create an index file that include each chain (chA chB ..) in mdp file i define energy groups such that: energygrps = chA chD for grompp i used this command: gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr but i got this error:

Re: [gmx-users] Calculating Distance

choose a atom, then calculate the transition vector of it with use of the initial and final coordinate. On Mon, May 16, 2016 at 11:50 AM, Sanket Ghawali wrote: > Dear, gmx-users, > > Hello everyone, > I'm simulating a peptide in an SDS micelle. The simulation was >

[gmx-users] calculate electrostatic force

Hi to all, i have two peptides that bind together, how i can calculate the electrostatic forces between these peptide atoms? tnx :) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] what means of contact in mindist?

ically 0.6 > nm). > > Cheers, > > Tsjerk > > On Mon, Feb 1, 2016 at 1:08 PM, masoud keramati <keramati.ma3...@gmail.com > > > wrote: > > > Hi all > > > > what means of "number of contact" in gmx mindist command? > > > > wha

Re: [gmx-users] what means of contact in mindist?

Hi i mean interactions between hydrophobic residues in a protein-ligand complex. On Mon, Feb 1, 2016 at 5:06 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > First, what do you mean by a "hydrophobic interaction?" > > Mark > > On Mon, F

[gmx-users] what means of contact in mindist?

Hi all what means of "number of contact" in gmx mindist command? what we can understand from it's result? Best -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Cannot write trajectory frame

i just install the 64bit linux and problem solved :-) On 1/4/16, masoud keramati <keramati.ma3...@gmail.com> wrote: > tnx dear Mark for your respond ;-) > + > Dear teemu > yes my OS is 32-bit and version of gromacs is 5.x > with installing 64bit OS, can i solve this probl

Re: [gmx-users] Problem using gromacs

in OPLS ff when i use tip3p water i got this error but if tip3p selected then there no problem and it's interesting! On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul wrote: > > > On 1/4/16 4:27 AM, soumi wrote: > >> Respected Sir, >>I am new user of gromacs.

Re: [gmx-users] Cannot write trajectory frame

gt; have disks formatted accordingly. > > > > Mark > > > > On Sun, Jan 3, 2016 at 1:22 PM masoud keramati < > keramati.ma3...@gmail.com> > > wrote: > > > > > yes that's true .. and i'm searching for a way to remove this > limitation > >

[gmx-users] Cannot write trajectory frame

Hello and happy new year! i have seen this issue in archive, the problem is with .trr size that can not reach more than 2GB and i think that is my problem too. my question is ,can i write .trr file with another file name and then finally append them? is it a true way? tnx for your responding

Re: [gmx-users] Cannot write trajectory frame

system. Get > a real one! :-) > > Mark > > On Sun, 3 Jan 2016 11:17 masoud keramati <keramati.ma3...@gmail.com> > wrote: > > > Hello and happy new year! > > > > i have seen this issue in archive, > > the problem is with .trr size that can not reach mor

Re: [gmx-users] Extending simulations

sorry with my question is it true that for extending simulation use the following code? gmx grompp -f md.mdp -c md.gro -t md.trr -p topol.top -o md2.tpr gmx mdrun -deffnm md2 *md.gro and md.trr is files for first run On 12/22/15, Justin Lemkul wrote: > > > On 12/21/15 7:00

[gmx-users] high temperature molecular dynamics

Hi to all is there any guide for high temperature molecular dynamics simulation? i want to use this method for unfolding process. thank for your respond :-) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] high temperature molecular dynamics

tnx dear David On 12/22/15, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > On 22/12/15 10:58, masoud keramati wrote: >> Hi to all >> >> is there any guide for high temperature molecular dynamics simulation? >> i want to use this method for unfolding proc

[gmx-users] Writing checkpoint

hi to all in the mdrun log file i see "Writing checkpoint, step 47840 at Tue Dec 8 18:42:52 2015". what means of this Writing checkpoint? -- 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] Writing checkpoint

can i run gromacs in parallel using two different computers? On 12/8/15, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/8/15 10:17 AM, masoud keramati wrote: >> hi to all >> >> in the mdrun log file i see "Writing checkpoint, step 47840 at Tue De

Re: [gmx-users] Writing checkpoint

ok tnx for ur respond On 12/8/15, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/8/15 11:36 AM, masoud keramati wrote: >> can i run gromacs in parallel using two different computers? >> > > I think you should spend some time reading the manual,

[gmx-users] LINCS WARNING

Hi to all dear gmx users during the Energy Minimization i got this warning in first few steps after step 20 "step 20: Water molecule starting at atom 34209 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate." but after 3021 steps it was converged to Fmax < 1000.

Re: [gmx-users] combine two pdb files

t; -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of masoud > keramati > Sent: Saturday, November 28, 2015 1:12 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] combine

Re: [gmx-users] combine two pdb files

eorders them and renumbers them after adding hydrogen > atoms. Did you try it? > > Regards, > Peter > > Sent from my iPad > > > On 27 בנוב׳ 2015, at 22:28, masoud keramati <keramati.ma3...@gmail.com> > wrote: > > > > Hello > > > >

[gmx-users] combine two pdb files

Hello I want to simulate two proteins and need to combine these two pdb files in one. important thing is the atom number. if combine with cat command it gives a file that contain two atom with the same atom and residue number that will make an error in simulation. is there exist any way to