Re: [gmx-users] RE: simulation of a metal binding sites

...@gmail.com said: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. -- Dr. Marc Baaden - Institut de Biologie Physico

[gmx-users] Optimizing system size by moving from rectangular to hexagonal cells

Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Suggestions for 3D-monitor/glasses for visualizing GROMACS output

very much any suggestions. Thanks very much for your help! Dean -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

Re: [gmx-users] Pulling a CG protein

field for the kind of simulation you are doing. This CG model has not been tested at all for this and it might not be very good at it! But I would be very interested in knowing how it actually perform. XAvier. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa

Re: [gmx-users] Pulling a CG protein

particularly well with respect to pulling simulations (although many people have used them for such simulations). The gold standard should probably be to compare CG pull simulations directly to corresponding experimental data whenever possible. So have even more fun :) Marc -- Dr. Marc Baaden

Re: [gmx-users] crystals of KCl during simulation

recently [1]. Marc Baaden [1] Interactions between neuronal fusion proteins explored by molecular dynamics, Biophys.J.94, 2008, 3436-3446. http://dx.doi.org/10.1529/biophysj.107.123117 -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http

Re: [gmx-users] Re: MD with RMSD restraint

at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Marc Baaden -- Dr. Marc Baaden - Institut de

Re: [gmx-users] running multiprocessor jobs on leopard 10.5.2

gromacs using open mpi (we didn't have to use any extra flags, as everything was in standard locations)all should work just fine. We used fftw3.1.2, gfortran and gcc. We are running on a 2x quadcore (3.0 GHz) mac pros. Will post some benchmarks soon. Best wishes, -Syma -- Dr. Marc

[gmx-users] Postdoc position available (virtual reality, interactive simulations)

of motivation as PDF document to [EMAIL PROTECTED] Please include the names of three referees. When? 3 years starting Jan 2008 Where? Laboratoire de Biochimie Theorique, Paris, France Salary: 2500 Euro/month Project Leader: Marc Baaden Website: http://www.baaden.ibpc.fr/projects/fvnano -- Dr. Marc

[gmx-users] Simulation cell rotation and CRYST1/periodic box information

wonder whether this could have something to do with the other 6 parameters on the line, but I don't quite know what they are and how they need to be adapted with respect to the rotation that I have applied. Any help would be appreciated, thanks in advance, Marc Baaden NB: is there is a tool

Re: [gmx-users] how to calculate internal energy for energygroups?

. You don't mess with the atom definitions however. For speed, turn off evaluation of all the non-bonded interactions somehow. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33

Re: [gmx-users] how to calculate internal energy for energygroups?

this does make sense and provides at least one reason to implement such a procedure. Marc -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217

[gmx-users] how to calculate internal energy for energygroups?

and Coulomb, but none for bonds, angles and dihedrals. Is there another way than using energy groups and g_energy for this purpose? Thanks in advance, Marc Baaden NB: I am using Gromacs 3.3.1 -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED

Re: [gmx-users] how to calculate internal energy for energygroups?

wrong. Bob Johnson -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ gmx-users mailing listgmx

Re: [gmx-users] how to calculate internal energy for energygroups?

-rerun with this tpr and xtc file and should be able to use g_energy to extract bond, angle and dihedral terms for my subselection.[..] This should work. It does up to mdrun -rerun, which yields a segmentation fault :( Marc -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique

[gmx-users] Replica exchange and freeze groups?

. Is there any trouble to be expected for combining these two options? Does anybody have experience with such an approach? Thanks in advance, Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX

Re: [gmx-users] simulation at particular pH

such that they correspond to the pH your are interested in. Equilibrium exchange of protons between aminoacid sidechains is probably happening on a timescale much longer than a typical simulation length. Gerrit -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED

[gmx-users] Re: (A problem with GROMACS)

. “WARNING: atom names in .top and .gro don’t match (NA-Na),…” I would be glad if you help me in this case. Thank you very much. Sincerely yours, Jahanshah Ashkani -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http