Re: [gmx-users] problems about trjconv

Quoting Di Pan <[EMAIL PROTECTED]>: > Hi, All > > I do my md simulation for 30ns, but after 20ns the protein move out of > the box, so it seems that the protein is broken in .trr file. I try to > use trjconv to put the protein back into the box and make the protein > whole. The command is like bel

[gmx-users] problems about trjconv

Hi, All I do my md simulation for 30ns, but after 20ns the protein move out of the box, so it seems that the protein is broken in .trr file. I try to use trjconv to put the protein back into the box and make the protein whole. The command is like below: trjconv trjc -f *.trr -o out.trr -s *.tpr -

Re: [gmx-users] Re: gmx-users Digest, Vol 43, Issue 81

servaas michielssens wrote: Thanks for your help, I checked the perl script (amb2gmx.pl) it should work for a solvated protein. The solvend and box are converted to gromacs but the box information is not converted as it should, amber only defines d and 3 angels (+information in the topology t

Re: [gmx-users] Problem in starting make hole

nur avneet wrote: Sir i want to use makehole program (gromacs 3.1.4)and i used the grompp command on dmpc.pdb with position restraints as specified in the tutorial. the position restraint file is as follows : [ position_restraints ] ; atom type fx fy fz 8 1 0.0

[gmx-users] Problem in starting make hole

Sir i want to use makehole program (gromacs 3.1.4)and i used the grompp command on dmpc.pdb with position restraints as specified in the tutorial. the position restraint file is as follows : [ position_restraints ] ; atom type fx fy fz 8 1 0.0 0.0 1000.0

[gmx-users] Re: gmx-users Digest, Vol 43, Issue 81

Date: Wed, 21 Nov 2007 14:03:53 -0800 From: "David Mobley" <[EMAIL PROTECTED]> Subject: Re: [gmx-users] restart an amber run in gromacs To: "Discussion list for GROMACS users" Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1 Hi, servaas michielssens wrote: > I use

[gmx-users] NOE distance restraints

Dear Gromacs users, I intend to perform a MD simulation of a GPCR model applying distant restraints to the backbone of alpha helices, something like NOE distance restraints. I guess that gromacs can't do it directly but if I've well understand I can manually provide classical distance restraints i

[gmx-users] Re:Re: gromacs preformance versus amber (David van der Spoel)

Message: 1 Date: Wed, 21 Nov 2007 21:54:57 +0100 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] gromacs preformance versus amber To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed servaas michi

Re: [gmx-users] restart an amber run in gromacs

Hi Servaas, In addition to the other remarks, also consider what happens to your system when you instantly go from discarding all interactions beyond 8 angstrom to including all interactions in the periodic system (with PME). Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecu