Re: [gmx-users] freeze water

What procedure will be better? Freeze or position restrain? Anthony On Monday 01 May 2006 7:17 am, Anthony Cruz wrote: On Friday 28 April 2006 12:02 pm, David van der Spoel wrote: Anthony Cruz wrote: Hi: I want to make a simulation of a small pepetide in a box of water but I want to

[gmx-users] top file popc

hi i run pdbgmx2 for popc but errore message is here: wrong format is in ffg43a2.h line 2 7 ow whould you please help me? thanks mahboobeh __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

RE: [gmx-users] segmentation fault in mdrun when using PME

-Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a

Re: [gmx-users] segmentation fault in mdrun when using PME

Diane Fournier wrote: -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and

[gmx-users] fudgeLJ / fudgeQQ are multiplicative factors

Perhaps someone can add this to the next update of the manual (on page 101?) Without going to Jorgensen's 1988 JACS paper it is difficult to be sure that fudge means multiply and not divide, especially given the most common usage of the word factor and that e.g. Berger Biophys. J. 1997 indicates

[gmx-users] top file popc

Send more information. what .itp and .top files are you using? what was your pdb2gmx command? what were the 3 or 4 lines on either side of the error message (cut and paste them)? hi i run pdbgmx2 for popc but errore message is here: wrong format is in ffg43a2.h line 2 7 ow whould you

[gmx-users] GMX on 2xopteron Dual core

Hello friends! After reviewing the chart for GMX performance I purchased this 2x dual core opteron ,2.6GHz procesors and installed Fedora Core 4 (K8N-DL mother board). On booting up, the OS gives the message 'MP system not assigned by PSB bios structure. how do I overcome this problem? Would

[gmx-users] Hydrogen bonds with version 3.3.1

Dear gmx-users, I am trying to calculate hydrogen bonds with gromacs version 3.3.1 I would like to have a cutoff of 2.7 A between hydrogen and acceptor and an angle cutoff of 60 degrees. For that I'm using the following command: g_hbond -f simulation.trr -s topol.tpr -r 0.27 -a 60 -noda

[gmx-users] cis-trans isomerization in Ryckaert Bellemans dihedrals

Hi all, I am trying to perform FEP on a double ring structure such that I want to see cis-trans isomerization of the molecule by shifting the reference angle by 180 degrees. How can I apply this shift on RB parameters of my dihedral? I read the manual, but transformation of parameters into RB