[gmx-users] (no subject)

Your reported errors: 1..while running pdb2gmx warning :'FE2' not found in residue topology database... What force field are you using in pdb2gmx? look at that .itp file and the files that it includes (.itp file is prefaced by 'ff' and is in share/gromacs/top/ or similar directory) If you

[gmx-users] New website

The site looks nice. My only difficulty is that I like to sit on the users mailing list and press the refresh button my my browser every few hours to see the new comments. That now takes me back to the The gmx-users Archives page. It's a tiny problem, but when one is hoping for an answer and

[gmx-users] g_angle gets confused by switching default output file names.

g_angle -ov angaver.xvg :: yields average angle g_angle -ov angdist.xvg :: yields angle distribution My Gromacs-3.3 command was: g_angle -ov x.xvg -type dihedral -f traj.xtc -s topol.tpr -n my.ndx Easily avoided, just posting a notice. ___ gmx-users

[gmx-users] Genbox - Removal of Unwanted Waters

If I have a solvated membrane and I want to extend the z dimension and add new waters there, this is what I do. The script could be modified to get rid of new waters in any x/y/z dimensions (around line 41 of the script). 1. run genbox on initial.gro to create solvated.gro 2. cp solvated.gro

[gmx-users] Including and itp file, for a residue

CA is not a lipid type. look at dmpc.itp [ atoms ] ; id atype resnr resname anamecgnr chargemass 1 LC3 1 DMPC CN1 0 0.4000 15.0350 2 LC3 1 DMPC CN2 0 0.4000 15.0350 3 LC3 1 DMPC CN3 0

[gmx-users] lipid.itp LJ-1,4 values involving water

Does anyone know why lipid.itp contains [pairtypes] LJ-1,4 values including lipid atoms and OW or HW? I can understand their inclusion in [nonbond_params], but it seems as if this would never be required in [pairtypes]. *** In case anyone else is trying to merge lipid.itp and OPLSAA, here is

[gmx-users] Highest possible temperature in NPT?

It is not immediately clear how one would implement REMD with NPT. In the simplest instance, your monte carlo test would be based on unscaled volumes (that would later scale) and including data from some time period X after a move would lead to a non-maxwellian distribution that was overly spread

[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] OPLS modification between 3.3 and 3.3.1??

Thank you Erik and Mark for your assistance. Appologies that I reposted an old question. I will be more diligent about my searches in the future. Chris. ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] OPLS modification between 3.3 and 3.3.1??

Hello, ffoplsaa.rtp has changed in the 3.3.1 release. However, there are no references given and no special notification of this fact. I was wondering if anybody knows the references for this change. Here is the difference between the two distributions: diff

[gmx-users] tpbconv inexact restart due to nstxout!=nstenergy?

Hello, I have a 10ns trajectory and also a 5ns trajectory restarted from the 5ns point in the original trajectory. However, the runs diverge almost immediately (as judged by g_dist selecting one Calpha and one water molecule). The ensemble was NPT with PME electrostatics nstlist = 10

[gmx-users] Does mdrun know when other gromacs programs move its destination .xtc?

When an output .xtc destination of mdrun is backed up while the original version of mdrun is still running, does mdrun know and does the output get handled correctly? here is what happened to me: 1) mdrun produces traj.xtc 2) Beleiving that mdrun had died due to a hardware error, I restarted the

[gmx-users] re: Does mdrun know when other gromacs programs move its destination .xtc?

Fantastic! Just another reason to love and prefer Gromacs. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to

[gmx-users] open_xtc() returns zero

#include stdlib.h #include string.h #include typedefs.h #include xdrf.h #include gmxfio.h #include xtcio.h #include smalloc.h #include vec.h #include futil.h #include fatal.h Thanks, Chris Neale. ___ gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] Testing nonbonded list update time

To estimate the largest atomic displacement between updates of the nonbonded list (e.g. in order to verify that the rvdw/rlist options are appropriate) : (1) do a short run (~100ps) and save the trajectory every 10steps or however often the nb list is updated. (2) trjconv -pbc nojump (3) Use

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