[gmx-users] hi

hey have a look http://www.com-im6.net/finance/ Kowsar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

Re: [gmx-users] MD continuation

Hi,   if you want to continue the simulation, you'd better use tpbconv command to generate a new *.tpr, or if you are using grompp command you have also to have  -c previouse.tpr in the command line, there is no need for *.gro or *.top.  From: delara aghaie

Re: [gmx-users] comparing simulations with diffrent forcefields

Dear Justin,   Thank you very much for the reply   Sogol From: Justin A. Lemkul jalem...@vt.edu To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, May 28, 2012 6:06 PM Subject: Re: [gmx-users

Re: [gmx-users] g_rms -bm

Dear Justin   Thank you very muchh   Sogol From: Justin A. Lemkul jalem...@vt.edu To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, May 24, 2012 9:59 AM Subject: Re: [gmx-users] g_rms -bm

[gmx-users] g_rms -bm

Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered.  Does it mean that it is for the bonds

[gmx-users] g_rms -bm

Dear Users, I am trying to analyze a ligand-protein simulation results. I read in the manual that using g_rms command with –bm option produces a matrix of average bond angle deviations. And only bonds between atoms in the comparison groups are considered.  Does it mean that it is for the

[gmx-users] Spherical shaped box

Dear users,   I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command    trjconv_mpi  -f *.trr -s *.tpr -o *new.trr -pbc nojump   followed by     trjconv_mpi -f  new*.trr -s

Re: [gmx-users] Spherical shaped box

Dear Tsjerk   Thank you   Sogol From: Tsjerk Wassenaar tsje...@gmail.com To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 16, 2012 2:46 PM Subject: Re: [gmx-users] Spherical shaped

[gmx-users] *.ITP file

 Dear Users,  I am trying to generate an *.ITP file for a ligand I am studying using Prodrg server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar hydrogens) while the *.ITP file dispays 37 atoms and it does not display the double bond in the structure, which results in

Re: [gmx-users] problem with make_ndx

You should first make an *.itp file for DPPC, then include it in the *.top file. whatever that is not in GROMACS library should be defined to it. You would better see  http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf , hope it will help. From: Anushree

Re: [gmx-users] problem with volume equilibration

You'd better first your .top file, to see if you have included DPPC .itp file and also in the compound section. if it was ok, check the .ndx and look for the atom numbers of DPPC, after finding the atom numbers, make a group ( Like othe parts of .ndx; water, or protein,...) and name it DPPC.

Re: [gmx-users] problem with making index.ndx

Is  DPPC a ligand or a compound ? From: Anushree Tripathi anushritripa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, January 31, 2012 10:56 AM Subject: [gmx-users] problem with making index.ndx I am using gromacs

[gmx-users] box changes its shape !

Dear gmx-users,   Running MD, I faced a problem, after 1ps of modeling, the box changes its shape from  dodecahedron to rhomboid cube! and as a result some parts of  the protein gets out of the box. I fixed it with trjcon command but keep comming up. Would you mind telling me where this problem