RE: [gmx-users] Dihedral functions

The exact functional forms are given in the Gromacs manual, most likely in one of the earlier chapters. Andreas From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of AverettDevin [daver...@wisc.edu] Sent: 26 June 2009 22:42 To:

[gmx-users] install DSSP ???

Hi I want to install DSSP in my mac, tiger. I have searched the procedure of installing DSSP but still cannot install it sucessfully. 1. I go to this website http://swift.cmbi.kun.nl/gv/dssp/ to install the source codes and the Linux executable file dsspcmbi. I put both the source codes and

[gmx-users] Install DSSP= cannot execute binary file ???

1. I go to this website http://swift.cmbi.kun.nl/gv/dssp/ to install the source codes and the Linux executable file dsspcmbi. I put both the source codes and the executable file dsspcmbi in the same document. 2. follow the procedures in the website

[gmx-users] force

Hi, all, I was wondering about the force given by Gromacs. One is in the .trr and .tpr file. When I read then with gmxdump, they are all zeros: traj.trr frame 0: natoms= 24000 step= 0 time=0.000e+00 lambda= 0 box (3x3): box[0]={ 3.24900e+00,

[gmx-users] Input output file error

Hi Gromacs Users, I used gromacs in 2007 and have data of that and now want to used that data by making graphs but the following errors occured: 1) Input output file error. 2) Fatal error. version 40 with version 20 program. I think I used some version of gromacs 3.0.3 or other at

Re: [gmx-users] Input output file error

s lal badshah wrote: Hi Gromacs Users, I used gromacs in 2007 and have data of that and now want to used that data by making graphs but the following errors occured: Newer versions of gromacs can read old files. Just install the latest version. 1) Input output file error. 2) Fatal

Re: [gmx-users] force

So I would assume you never wrote any forces in your trr file. The mdp file option nstfout=0 is most probably set, isn't it ? If you use -pforce you realize, that forces arise in your simulation, but you do not tell gromacs to write them to a file. /Flo * Shuangxing Dai

Re: [gmx-users] force

The nstfout =1 in mdout.mdp. So this should not be where the problem is. - Original Message - From: Florian Dommert domm...@icp.uni-stuttgart.de To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, June 27, 2009 3:20 PM Subject: Re: [gmx-users] force

Re: [gmx-users] force

* Shuangxing Dai shuangxing...@gmail.com [2009-06-27 18:57:41 -0600]: The nstfout =1 in mdout.mdp. So this should not be where the problem is. So this was the most obvious mistake I could imagine and you see it is always appreciated that you put your mdp file also to the list, that everybody

Re: [gmx-users] force

Yes, they are all zeros. I am confused why this happen. Thank you for help. And here is the mdp file: ; RUN CONTROL PARAMETERS = integrator = steep nsteps = 50 ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout