Re: [gmx-users] losing data in trjconv?

trjconv, to copy also the forces in the original trr file. Best regards Lucio El lun, 15-10-2012 a las 21:18 +0800, Gil Claudio escribió: > Hi Justin, > > My original intention was to lessen the 5 ns trajectory to transfer to > another drive. I did > > trjconv -f traj.trr -o

Re: [gmx-users] losing data in trjconv?

t was not supposed to do anything, hence my surprise upon seeing the file size decrease by ~25%. No other flags were used. I'll do your suggestion in 2 days. Am out of the lab till then. Thanks Gil Claudio On Oct 15, 2012, at 7:55 PM, Justin Lemkul wrote: > > > On 10/15/12 7

Re: [gmx-users] losing data in trjconv?

Hi Peter, Same machine, all single precision. Gil Claudio On Oct 15, 2012, at 5:39 PM, "Peter C. Lai" wrote: > Was traj.trr output by the same machine/mdrun as the machine you are running > trjconv on? > > Is traj.trr (or the mdrun that wrote it) double precision and

[gmx-users] losing data in trjconv?

Hi all, When I do the following command trjconv -f traj.trr -o traj_1.trr the file size of traj_1.trr is around 25% smaller than traj.trr. Does traj_1.trr contain less data than traj.trr? Thanks Gil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/

[gmx-users] g_densmap per slice

between 1nm to 2nm? Thanks is advance. Gil Claudio Tonight's top picks. What will you watch tonight? Preview the hottest shows on Yahoo! TV. http://tv.yaho

[gmx-users] Re: Official charmm support

I would like to suggest that you include the carbohydrate force field of J Brady (CSFF). Here are some references and download sites Journal of computational chemistry 2002, vol. 23, no13, pp. 1236-1243 http://people.cs.uct.ac.za/~mkuttel/downloads.html Thanks Gil Claudio > Dear grom

[gmx-users] removing some solvent molecules

I have a simulation box with a polymer in the middle and solvent molecules surrounding it. The box ended up being much bigger than needed--I'll need to reduce its size from 20.0 nm to 15 nm, removing solvent molecules in the process. Is there a way to do this? Thanks. Gil Cl

[gmx-users] Re: gmx-users Digest, Vol 25, Issue 5

, at 9:48 AM, David van der Spoel wrote: > gil claudio wrote: >> I just derived the conversion of the dihedral >> constants from OPLSAA to RB and I get a set of >> equations different from the ones printed in the >> manual (3.3, p 56). >> C1 = V1 / 2 - 3 V3 / 2 >&g

[gmx-users] correction in oplsaa to rb conversion?

ow if what I did was correct. I can send the mathematica file to those interested in the derivation. Gil Claudio University of Asia and the Pacific __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yaho