Re: Sv: Re: [gmx-users] double and single precision

ion: Header: 964b, 1st frame: 240b, then 576 b/frame Double precision: Header+1st frame: 1376, then 1084 b/frame Thanks to Berk Hess who helped me a lot! /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS 033- 435 45 37 edvin.erdt...@hb.se D424 >>> 2012-02-20 k

Re: Sv: Re: [gmx-users] double and single precision

Hi again How do I "set the env.var. GMX_ENX_NO_FATAL"? I have tried in bash with: GMX_ENX_NO_FATAL=1 and then eneconv -e But I still get fatal error. /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS >>> 2012-02-20 kl. 09:38, skrev Mark Abraham

Sv: Re: [gmx-users] double and single precision

Hi So the best I can do now is to recreate the first part, and rerun "new" the simulations? /Edvin -- Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS >>> 2012-02-20 kl. 09:26, skrev Mark Abraham : > On 20/02/2012 7:19 PM, Edvin Erdtman wrote: >

[gmx-users] double and single precision

/Errors Can I do something to divide the file into a double and a single part? /Edvin Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] double and single precision

/Errors Can I do something to divide the file into a double and a single part? /Edvin Dr. Edvin Erdtman Instutitionen Ingenjörshögskolan 501 90 BORÅS -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

Sv: Re: [gmx-users] Add bridging residue

> "Justin A. Lemkul" wrote: > Please see the following: > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > Yes. I know all that! But my question was if there is a possibility to build a new residue which has a cross-link bond to another residue. How can I define

[gmx-users] Add bridging residue

Hi To the Amber force field I want to add a new residue, which is connected covalently to another residue in a protein (similar to a CYS-CYS bridge). Can I define this bond somewhere in the force field files (rtp, atp...) so that the inter-residue bond can be generated by pdb2gmx? Or do I have

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

protein that is the problem - need to be more minimized? /Edvin Justin A. Lemkul wrote: Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi again I don't know if you were aware of it, but I have commented some Justin's questions further down in the e-mail (my last e-mail wasn't onl

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

LINCS warnings. Thankful for all help! /Edvin Edvin Erdtman wrote: Hi again an Thank you for comments! Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been u

Re: [gmx-users] Error with equilibration of DPPC membrane with protein

Hi again an Thank you for comments! Justin A. Lemkul wrote: Edvin Erdtman wrote: Hi We have a problem of equilibrate the system with a protein within DPPC. We have used dppc128.pdb from Dr. Tielemans website. We have been using their perl script inflategro.pl to insert our protein. We

[gmx-users] Error with equilibration of DPPC membrane with protein

500 0 500 annealing_temp = 100 323 100 323 100 323 100 323 pbc = xyz optimize_fft = yes unconstrained_start = no - Thankful for all help we can get! /Edvin and Sujith -- Fil. Lic. Edvin Erdtman, PhD. student in Biophysi

[gmx-users] Cuted trr file not readable

e the precision of the file (that is the error I got, "can not determine precision of trn file"). Is it in any manner possible to restore, so the trr molecule can be used? /Edvin -- Edvin Erdtman Ph.D. student Department of Natural Sciences and Örebro Life Science Center Örebro Un

Re: [gmx-users] Error using double precision

> >Ok (you didn't say that in the first mail...). > >Does it also happen on one processor? > > I Haven't tested in d.p. > > >After how many steps does it happen? (see Marks mail). > > after 30 steps, that is 600 ps. > > > I energy minimized the system in d.p. and it is still running after

[gmx-users] Error using double precision

>Ok (you didn't say that in the first mail...). >Does it also happen on one processor? I Haven't tested in d.p. >After how many steps does it happen? (see Marks mail). after 30 steps, that is 600 ps. I energy minimized the system in d.p. and it is still running after 710 ps. _

[gmx-users] Error using double precision

an unequilibrated system. But it worked with single precision! Or do I need to make a energy minimization first in DP? ------- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1 Örebro Universitet S-701 82 Örebr

[gmx-users] Error using double precision

--- Aborting run after process-2 terminated abnormally Childprocess 17353 exited with exitcode 2 --- gcq#10922: Thanx for Using GROMACS - Have a Nice Day Thankful for some help. Edvin --- Fil. Mag. Edvin Erdtman Biofysikalisk kemi Naturvetenskapliga instutitionen Fakultetsgatan 1

Re: [gmx-users] g_dist problems

! Edvin Edvin Erdtman wrote: $ file /usr/bin/g_dist /usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped I copied the file to another machine. And there g_dist ran with no problem! - the above

Re: [gmx-users] g_dist problems

Edvin Erdtman wrote: Which compiler did you use? This maybe says more: $ file /usr/bin/g_dist /usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped I copied the file to another machine. And there

Re: [gmx-users] g_dist problems

Which compiler did you use? This maybe says more: $ file /usr/bin/g_dist /usr/bin/g_dist: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), stripped -Edvin ___ gmx-users maili

Re: [gmx-users] g_dist problems

David van der Spoel skrev: Edvin Erdtman wrote: Hi again... How can we tell? You haven't given us your command line, or a meaningful chunk of output. my command: g_dist -f traj.xtc -n index.ndx -s topol.tpr The output: --- Select a group: 0 Selected 0: 'DPPC' Select a gr

[gmx-users] g_dist problems

Hi again... How can we tell? You haven't given us your command line, or a meaningful chunk of output. my command: g_dist -f traj.xtc -n index.ndx -s topol.tpr The output: --- Select a group: 0 Selected 0: 'DPPC' Select a group: 1 Selected 1: 'AL' Reading frame 0 time0.000 Back

[gmx-users] g_dist problems

this: 216.1533.72626512.12824731.1397220 -2.8384237 216.50001533.7 Am I doing something wrong? I tried to convert the trajectory using trjconv -pbc, but non of the options seems to work. Edvin -- Edvin Erdtman Ph.D. student Department of Natural Sciences and Örebro Life