Re: [gmx-users] gen_vel

2009-12-04 Thread Mark Abraham
leila karami wrote: Hi in which case in mdp file, gen_vel should be yes or no? ... when you want to generate velocities or not. See manual section 3.4, particularly 3.4.1 Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sea

[gmx-users] gen_vel

2009-12-04 Thread leila karami
Hi in which case in mdp file, gen_vel should be yes or no? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use th

Re: [gmx-users] RE: Mark & Justin - grompp error for gmxtest-4.0.4 and 3.3.3 on new gromacs-4.0.5 install

2009-12-04 Thread Yirdaw, Robel Birru
Thanks Mark and Justin for all your input. I will try the git version and do any necessary modifications to test my install. > Yirdaw, Robel Birru wrote: >> Thank you both for your reply. >> >> So how did you guys verify and test gromacs on your machines? >> Mark, from your response, test-set 4

Re: [gmx-users] Re:Re: helix tilt

2009-12-04 Thread Mark Abraham
Stefan Hoorman wrote: Stefan Hoorman wrote: > How can I calculate the angle between a helix inserted in a membrane and > the axis perpendicular to the surface of the membrane. I have tried > using g_helixorient, but the graphs all come as a straight line in zero.

Re: [gmx-users] mpispawn.c:303 Unexpected exit status

2009-12-04 Thread Justin A. Lemkul
shivkumar bale wrote: Hi Gromacs Users, when I am trying to run the simulation I am getting the following error: mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE I read about this online and it says that simulation is running out of memory and

[gmx-users] mpispawn.c:303 Unexpected exit status

2009-12-04 Thread shivkumar bale
Hi Gromacs Users, when I am trying to run the simulation I am getting the following error: mpispawn.c:303 Unexpected exit status Child exited abnormally! Killing remote processes...DONE I read about this online and it says that simulation is running out of memory and it depends upon the grid sp

Re: [gmx-users] amber force field in Gromacs

2009-12-04 Thread Lucio Ricardo Montero Valenzuela
This kind of problems can occur if you were restraining atom positions and using pressure coupling. Best regards Lucio. Lucio Ricardo Montero Valenzuela PhD Student Laboratorio del Dr. Federico Sánchez Ext. 27666 Departamento de Biología Molecular de Plantas Instituto de Biotecnología, UNAM Cu

Re: [gmx-users] g_mindist after trjconv -fit give different results

2009-12-04 Thread Tsjerk Wassenaar
Hi Elad, This has been mentioned several times before, in a different context. But fitting only affects coordinates, and not the PBC. So after fitting the coordinates and the PBC don't match any more and any analysis requiring PBC, such as calculating minimal distances, will give garbled results.

Re: [gmx-users] dihedral restraints in gromacs 4.0.5

2009-12-04 Thread Justin A. Lemkul
Steven Ari Beasley wrote: has anyone successfully incorporated dihedral angle restraints in gromacs 4.0.5 protein simulation. i can only find instructions for gromacs 3.3.1, nothing in the manual. Do these instructions not work? http://www.gromacs.org/Documentation/How-tos/Dihedral_Rest

[gmx-users] dihedral restraints in gromacs 4.0.5

2009-12-04 Thread Steven Ari Beasley
has anyone successfully incorporated dihedral angle restraints in gromacs 4.0.5 protein simulation.   i can only find instructions for gromacs 3.3.1, nothing in the manual.  i don't know if the format is the same or whether it requires diffent .mdp flags, but so far i have not been able to suc

[gmx-users] g_mindist after trjconv -fit give different results

2009-12-04 Thread eladp
Hi all, I have a system of protein+water+ions. I measured the minimum distance between one of the ions to the protein. Afterwards I fitted the trajectory using g_trjconv -fit rot+trans Did the same mindist again and the graphs are not always identical. Any suggestions? I use gromacs 4.0.5 wit

Re: [gmx-users] Exclusions in topology file seem not working for big systems

2009-12-04 Thread Reza Salari
Thanks for your response. I see that what I want to do is a little bit unusual. It is part of a bigger picture that also include implicit water calculations and the main goal is to look into the effects of water models on the results, not necessarily trying to reproduce the experimental results

[gmx-users] Re:Re: helix tilt

2009-12-04 Thread Stefan Hoorman
> Stefan Hoorman wrote: > > How can I calculate the angle between a helix inserted in a membrane and > > the axis perpendicular to the surface of the membrane. I have tried > > using g_helixorient, but the graphs all come as a straight line in zero. > > See -z in g_sgangle -h > > Mark > > > Thank y

Re: [gmx-users] xmgrace

2009-12-04 Thread Justin A. Lemkul
pawan raghav wrote: While running MD simulation I have number of queries mentioned below: 1. When executing xmgrace command it returns the bash command not found, then how to install GRACE package on windows? Visit the Grace website and follow whatever download and installation instructio

[gmx-users] xmgrace

2009-12-04 Thread pawan raghav
While running MD simulation I have number of queries mentioned below: 1. When executing xmgrace command it returns the bash command not found, then how to install GRACE package on windows? 2. When defining the box dimention then how do I know about the distance of protein (207 residues) from the b

RE: [gmx-users] LIE method

2009-12-04 Thread osmair oliveira
Hi Tatiana, If you just want to estimate the binding energy, I suggest that, initially, you use docking methodologies. For example, you can use AutoDock program, that is a free program. I hope this help Osmair Brazil > Date: Fri, 4 Dec 2009 09:25:56 +0100 > From: r.fried...@bioc.uzh.ch > To:

RE: [gmx-users] Exclusions in topology file seem not working for big systems

2009-12-04 Thread Berk Hess
Hi, I don't know. I have not understood what you want to do. On the physical level, there is no distinction between intra-molecular bonded and non-bonded interactions. So this makes me suspect that what you are trying to do is incorrect, independently of if you remove the 1-4's or not. Berk Dat

RE: [gmx-users] RF and TI

2009-12-04 Thread Berk Hess
Hi, Yes, RF in the couple scheme is correct. The "manual" calculation you did is incorrect. In the decoupled state the intra-molecular interactions of the decoupled molecule should not be RF, but plain Coulomb. The couple option does this correctly. Berk > Date: Fri, 4 Dec 2009 15:52:58 +0300 >

[gmx-users] RF and TI

2009-12-04 Thread Alexey Odinokov
Dear gmx users, I calculated the hydration free energy of benzene molecule two times. First time I used a decoupling method implemented in GROMACS. Second time I performed thermodynamical integration between different topologies of the benzene molecule: non-interacting with media and normal one. Al

Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?

2009-12-04 Thread ms
Justin A. Lemkul ha scritto: As per the title. I need to understand what is the difference to help myself debug my inane efforts at CG parametrization. LJ(1-4) I think is clear (non bonded, non-coulombic interactions between 1-4 pairs described in the topology), but about the re

Re: [gmx-users] Re: 1-4 interaction energies in g_energy

2009-12-04 Thread Mark Abraham
Vitaly V. Chaban wrote: Hi, Please suggest why is the reason that 1-4 term is not displayed (to be selected for calculation) in the g_energy utility? I have two kinds of objects (with 25 and 5 atoms) in my system - with "nexcl" equal to 3 and 2. I guess the 1-4 term may not be displayed if there

[gmx-users] Re: amber force field in Gromacs

2009-12-04 Thread servaas
Hi Alan, Thank you for all your efforts. This is getting strange, I tried following your procedure below but is still does not work for me: step 3500, will finish Fri Dec 4 09:56:51 2009Warning: 1-4 interaction between 6 and 10 at distance 1.454 which is larger than the 1-4 table size 1.000 nm

Re: [gmx-users] LIE method

2009-12-04 Thread Ran Friedman
Dear Tatiana, In principle you can estimate binding free energy differences using LIE (or LIECE). Your success will depend on the protein and proper parameters. The best way is to try ligands with known binding energies at first. Check the relevant literature for details and parameters. Ran. --