[gmx-users] g_analyze -ee

Dear all I used g_analyze -f dist.xvg -ee In the one of the my output files, I encountered Read 1 sets of 1252 points, dt = 0.0119951 std. dev.relative deviation of standard - cumulants from those of set

Re: Fw: [gmx-users] trjconv in martini

Hi Sara, Please find the script as attachment. When saved, you have to make it executable using chmod +x xtcrev.py Then it should work... Cheers, Tsjerk On Sat, Dec 31, 2011 at 5:59 AM, mohammad agha mra...@yahoo.com wrote: Hi Tsjerk, Thank you for your reply, yes it is #!/usr/bin/env

Re: Fw: [gmx-users] trjconv in martini

Hi Tsjerk, Thanks for your reply, yas, I did this too! Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 11:42 AM Subject:

Re: Fw: [gmx-users] trjconv in martini

Hi Tsjerk, Thanks for your reply, yes, I did this, too! but my problem wasn't solved! Best RegardsSara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday,

Re: Fw: [gmx-users] trjconv in martini

Hi Sara, You do have python installed, don't you? Maybe you have to have version 2.5 or 2.6 for this to work, although I think it's not using any features that were not already in 2.3 or 2.4. Can you post the workflow you're trying now, pasting the exact commands you use? Cheers, Tsjerk On

Re: Fw: [gmx-users] trjconv in martini

Hi Tsjerk, Thank you very much from your reply, I think you're right, my problem is about python installation, I take error when I want to install python 2.5 and 2.6, now I am installing the python 2.3. My workflow is according to what you said me means: # Get a clustered reference frame

Re: Fw: [gmx-users] trjconv in martini

Hi Sara, # Extract the first part of the trajectory trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1 That should be -e 19 :) But you can also use -e 20. Probably that is better. I first thought it'd be better to avoid a double frame, but since trjcat is used to combine the

Re: Fw: [gmx-users] trjconv in martini

Hi Tsjerk, Thank you very much from your help. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 3:41 PM Subject: Re: Fw:

[gmx-users] After installation help

Hello buddies, I'm a very beginner in gromacs and I just got a trick but simple situation (for you :D). After the installation of my gromacs on ubuntu 11.10 I opened the .bashrc file and put the following code in the following place as instructed by installation session on the webpage: .BASHRC

Re: [gmx-users] Configurations stored in REMD trajectories

Thanks :D 2011/12/30 Mark Abraham mark.abra...@anu.edu.au On 31/12/2011 7:03 AM, César Ávila wrote: Dear all, perhaps someone can help me with this doubt. When a REMD simulation is run, which configuration is stored for any given replica, the one before the exchange or the one that we get

[gmx-users] Re: cnt topology

I hope you understand that I canNOT fix the problem by just looking at several thousands on numbers in your topology... My preliminary guess would be that the problem is localized in the dihedral section, i.e. you don't define all the necessary dihedrals or define some of them inconsistently with

[gmx-users] detective work before or after creating a topology?

Hello I have two questions. First question: If you parameterize a force field (which means that you make changes in atomtypes.atp, create a new .rtp and a .hdb file, make changes in ffnonbonded.itp, create a residuetypes.dat file and finally make symbolic links to gromacs) and you use pdb2gmx

Re: [gmx-users] detective work before or after creating a topology?

On 1/01/2012 7:45 AM, Lara Bunte wrote: Hello I have two questions. First question: If you parameterize a force field (which means that you make changes in atomtypes.atp, create a new .rtp and a .hdb file, make changes in ffnonbonded.itp, create a residuetypes.dat file and finally make

[gmx-users] Obtain the flux of water

Dear all,  Whether there is a program in Gromacs that would directly or indirectly obtained the flux of water ? How to obtain the flux water in Gromacs ?  Best Regards  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] Re: Hi, May I ask you a question about the free energy calculation tutorial?

yywang wrote: At 2011-12-31 04:42:12,Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: yywang wrote: Dear Justin Lemkul, I find a tutorial about the free energy calculation by g_bar in Gromacs. (