Re: [gmx-users] xtc file

Moeed wrote: Dear experts, I am trying to exclude all nonbonded interaction on hexane molecule. 1-For the md -rerun command I do not know how to get the input XTC file. the program is expecting rerun.xtc mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o ORIGINAL-Trajectory-NO

[gmx-users] xtc file

Dear experts, I am trying to exclude all nonbonded interaction on hexane molecule. 1-For the md -rerun command I do not know how to get the input XTC file. the program is expecting rerun.xtc mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-

Re: [gmx-users] Re: OPLS-AA/L force field

you zou wrote: Hi, Thank you for your help.Now there is this question that I have just .pdb file and when use protonate command it is" protonate -f drg.pdb -o drg.gro", this is without hydrogens atoms too. I think something is wrong, but I don't know what it is.In definition of "protonate" th

[gmx-users] Re: OPLS-AA/L force field

Hi,Thank you for your help.Now there is this question that I have just .pdb file and when use protonate command it is" protonate -f drg.pdb -o drg.gro", this is without hydrogens atoms too.I think something is wrong, but I don't know what it is.In definition of "protonate" there is "protonate r

Re: [gmx-users] rerun trajectory does not match input file

Thanks Justin! On Sat, May 22, 2010 at 10:12 AM, Justin A. Lemkul wrote: > > > John Shultz wrote: >> >> Why do I get this message saying the group is empty? >> >> >> >> Analysing residue names: >> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat >> There are: 11350      OT

Re: [gmx-users] rerun trajectory does not match input file

John Shultz wrote: Why do I get this message saying the group is empty? Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244PROTEIN residues There are: 0DNA residues Analysing P

Re: [gmx-users] rerun trajectory does not match input file

Why do I get this message saying the group is empty? Analysing residue names: Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat There are: 11350 OTHER residues There are: 244PROTEIN residues There are: 0DNA residues Analysing Protein... Analysing Oth

Re: [gmx-users] rerun trajectory does not match input file

John Shultz wrote: Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Yep, that's the purpose of make_ndx. -Justin Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul wrot

Re: [gmx-users] rerun trajectory does not match input file

Justin, I finally got a chance to get back to this. I read the make_ndx instructions. Unless I am mistaken, I guess that is what you use to merge groups. Thanks, Jack On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul wrote: > > > John Shultz wrote: >> >> Thank you Justin, is there a way I can

Re: [gmx-users] the output of do_dssp

Hsin-Lin wrote: Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way: -- @ s0 legend "Structure" @ s1 legend "Coil" @ s2 legend "Bend" 0514 1 --- My system is dimer and each peptide

Re: [gmx-users] shake and settle

- Original Message - From: subarna thakur Date: Saturday, May 22, 2010 19:23 Subject: [gmx-users] shake and settle To: gmx-users@gromacs.org --- | > Hi gmx user > I want to use shake algorithm for bonds within protein and settle a

[gmx-users] shake and settle

Hi gmx user I want to use shake algorithm for bonds within protein and settle algorithm for the bonds of the water. How do I specify two different constraints algorithm in pr.mdp file?  Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

[gmx-users] the output of do_dssp

Hi, I use do_dssp to generate xvg file collect the last line to make a plot. There are something written in this way: -- @ s0 legend "Structure" @ s1 legend "Coil" @ s2 legend "Bend" 0514 1 --- My system is dimer and each peptide has 6 residue. And th

Re: [gmx-users] list of published papers

On 2010-05-22 06.53, Mark Abraham wrote: http://www.gromacs.org/Documentation/Gromacs_papers - Original Message - From: milad ekramnia Date: Saturday, May 22, 2010 14:14 Subject: [gmx-users] list of published papers To: gmx-users@gromacs.org > Dear Gromacs users > I can remember up t

Re: [gmx-users] g_clustsize output

On 2010-05-22 00.28, toma0...@umn.edu wrote: Hello, Thanks for the response. g_clustsize outputs two xpm files of the weighted and non-weighted cluster size vs time. Is there another way for me to get number of clusters vs cluster size? Not without programming, but since the information is there