[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" mailto:jalem...@vt.edu>> wrote: yywang wrote: Dear Justin Lemkul, I find a tutorial about the free energy calculation by g_bar in Gromacs. ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_

[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 a

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 symbo

Re: [gmx-users] After installation help

On 31/12/2011 11:58 PM, Willian Pereira Felix wrote: 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 inst

[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

[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] Re:

Zahra: I believe the problem is in your topology (*.TOP) file which you don't attach. From your pictures, we see that the system does not survive energy minimization, so the intramolecular interactions are not simulated wisely. Happy New Year, Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept

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

Thanks :D 2011/12/30 Mark Abraham > 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 after the exch

[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 fi

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

Hi Tsjerk, Thank you very much from your help. Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Saturday, December 31, 2011 3:41 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, > # Extract

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 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 trjc

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 Sat

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 To: mohammad agha ; Discussion list for GROMACS users Sent: Saturday, December 31, 2011 11:42 AM Subject: Re: Fw: [gmx-users] trjc

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

Hi Tsjerk, Thanks for your reply, yas, I did this too! Best Regards Sara From: Tsjerk Wassenaar To: mohammad agha ; Discussion list for GROMACS users Sent: Saturday, December 31, 2011 11:42 AM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, Ple

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 wrote: > Hi Tsjerk, > > Thank you for your reply, yes it is #!/usr/bin/env python > May I as

[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