[gmx-users] DMSO-protein simulation
Dear Users, I am trying to do a DMSO-protein simulation.As I have posted this query earlier also and got one suggestion of adding atomtypes section in dmso.itp file that is not present in it.The problem I am facing here is: how to calculate c6 & c12 coloumn for DMSO thanx in advance -- PRASUN (ASHOKA) ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Gromacs 4.0 beta1
Sagittarius wrote: What is the link to download binaries and source code for Gromacs 4.0 beta1? It is still in development, so you have to retrieve it from CVS: http://wiki.gromacs.org/index.php/CVS_HowTo -Justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Gromacs 4.0 beta1
What is the link to download binaries and source code for Gromacs 4.0 beta1? ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: Time step in md
On Sat, Sep 20, 2008 at 10:29, Vitaly Chaban <[EMAIL PROTECTED]>wrote: > > could you explain my the secret of choosing to time step for md > > integrator? > The secret is, to have the timestep small enough so that you could "truly" say between two consecutive steps the forces are linear, and to have it large enough so the computation would be feasible. Other then that, look at the previous answers you got for a more "hands on" approach. You might also want to read about integrating MD. --Omer Markovitch. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: Time step in md
> Hello, > could you explain my the secret of choosing to time step for md > integrator? I want to perform a 10-20 ns simulation in water in order > to, for ex., calculate some interactions or to see if the structure > would relax to a stable state. > If I use vsites, heavyh and LINCS I can run with 6 fs step. This would > be quite quick. > I just wonder if this is `by book`. > I appreciate your help. Hi Dimitry, `by book` is when the error caused by discrete timestep is not significant for your particular system. The standard timestep for water I believe is 2 fs (or 1 fs is also popular). If you want using the bigger value I would suggest to perform the single calculation with dt=2fs and the dt you want and compare the basic system parameters. It will determine if anything is wrong due to the timestep. -- Vitaly V. Chaban School of Chemistry National University of Kharkiv Svoboda sq.,4, Kharkiv 61077, Ukraine email: [EMAIL PROTECTED] skype: vvchaban tel.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Peptide aggregation
Dear Leon, Note that you can already use g_clustsize to check the aggregates. I'll contact you off list next week with the modified version. Ran On Fri, 19 Sep 2008 17:13:02 +0100 Léon Salgado <[EMAIL PROTECTED]> wrote: Dear Dr. Ran Friedman Would you please be so kind to send me your version, to calculate then the rgyr "of the largest aggregate". The box was built with a layer of 1.2 nm around the solute (editconf -d 1.2). Leon Ran Friedman wrote: Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apart. A rough estimate can be taken from the gyration radius for all the peptides together. Already did a trjconv -pbc nojump pre-treatment on the trajectory, before calculating the Rgyr. The gyration.xvg plots sometimes do show abrupt jumps, and this is surely due to boundary effects, if I correctly understood the PBC idea. If a peptide approaches the boundary, it appears on the opposite side, thus rgyr will show a false sudden increase. In fact, the peptide could be closer to the rest of the other peptide molecule(s). Thus my question is: how to deal with peptide clusters that span over the periodic boundaries? A similar question was done by Singh: http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html and it was suggested by Chris Neale to pre-process the trajectory (see http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). Best, Léon ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RE: ligand parameterization for amber port in gmx
What do you mean by severe deformations? I would expect a lagere difference in conformation for pyrophosphate bound to mg and free pyrophosphate. You could do extra quantum calculations and compare them to your force field calculations to check the quality of your force field. If this is no good, you could consider using RESP charges. Did you compare your parameters do published pyrophosphate parameters e.g. http://www.pharmacy.manchester.ac.uk/bryce/amber hope this helps, servaas > Dear people, > > I have parameterized a ligand with one phosphate and one pyrophospate group > using antechamber with AM1-BCC charges and the GAFF forcefield. Amber files > were converted to gmx files (*.itp/*.top and *.gro) with the amb2gmx > conversion tool (http://www.alchemistry.org/wiki/index.php/Free_Energy_Tools) > and then used in gromacs for energy minimization. The geometry looks fine > after in vacuo EM and EM in water (ffamber tip3p model from amber ports) of > the ligand alone (not bound to protein!). Minimizing the ligand in its > binding mode as seen in the corresponding PDB (using the amber03 ff) also > works fine if magnesium ions are NOT included. Including magnesium ions > however leads to severe deformations of the phosphate and pyrophosphate > groups. I suspect it has something to do with not including the magnesium > ions in the parameterization. Can anybody please give me a hint on how to > solve this problem? > > Thanks a lot, > Merc ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
