[gmx-users] Changing output frequency when doing a continuation with tpbconv

Hi I was wondering if you can change the output frequency of coordinates written to the *.trr file when you are doing continuation runs using tpbconv. Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED

[gmx-users] Question about use of tpbconv

run3 files by concatenated and then a run4 file generated using the complete edr and trr files. Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users

[gmx-users] Using tpbconv

coupling. Is it still appropriate to use tpbconv? Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

[gmx-users] Temperature averages and log files

using these methods are fine (i.e the are v close to what I have asked them to be), in the AVERAGES section of my log files these values are just plain weird e.g. temp of 1.78+01 and such. I really don't think I have done anything wildly stupid, so could someone reassure me? Thanks Jo Jo

[gmx-users] Ions close to protein

Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe reques

[gmx-users] self made topology and fmax

strange as I don't have an atom 80. Has anyone ever observed this before or does anyone have any ideas as to what the cause of this is? Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROT

[gmx-users] aromatic hydrogens

the ffG43a2 force field. Many thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] ffG43a2 and vdw

Hi In the manual (page 81) it mentions that when using a Gromos96 ff the LJ cut-off should be set at 1.4nm or more, I have been using 1.0nm, should this cause many problems? Thanks Jo Joanne Hanna Department of Chemistry University of Warwick Coventry CV4 7AL (02476) 574623 [EMAIL PROTECTED

[gmx-users] compiling on fedora

uninitialized in this function discopar.c: In function ?disco_slave?: discopar.c:231: warning: ?xcenter? may be used uninitialized in this function Is this something to be concenred about? and if so, how can i work around this? Thanks J Joanne Hanna Department of Chemistry University of Warwick Cov

[gmx-users] compiling with gcc

: warning: 'max1_6' may be used uninitialized in this function gmx_rmsdist.c:544: warning: 'max1_3' may be used uninitialized in this function eneconv.c: In function ?main?: eneconv.c:411: warning: ?nremax? may be used uninitialized in this function eneconv.c:415: warning: ?timestep?