[gmx-users] g_covar ends up complaining from a Segmentation Fault

dited nothing myself though and all files were made by GMX programs themselves! Would be nice if I could get some comments, in case anyone has encountered this before. Thanks in advance, greetings Peyman -- Peyman Yamin Computational Structural Biology Group Institut fuer Strukturbiologie und B

[gmx-users] Mailing list and multiplicity

file of popc, which read something like this: [ dihedrals ] ; aiajakal funct phi0 cp mult .. .. 22232425 190-5.685 0 .. .. Thanks, Cheers, Peyman -- Peyman Yamin Computational Structural Biology Group Institut fuer Strukturbiologie

[gmx-users] merge two PDBs

mer! What should one do at all, if one gets a NMR- based PDB which has the structure of more than one chemically equal species and wants to work with it? With Herzian thanks... Cheers, Peyman -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschu

Re: [gmx-users] Parallel installation core2 quad -mpi?

Hey Mark, thanks for the swift reply. I installed 4.0.5 now. with the same testset it failes this time on some of the kernel tests though all pdb2gmx ones pass. As far as I understood, I should simply ignore it? I didn't use --enable-mpi but when I run test script with -np 4, it does the job

[gmx-users] Parallel installation core2 quad -mpi?

3,  step  50:     -36.2929 Files read succesfully -- Peyman Yamin Institut fuer Strukturbiologie und Biophysik (ISB) ISB-3: Strukturbiochemie Forschungszentrum Juelich D-52425 Juelich Tel:(49)-2461-61-2875 Fax:(49)-2461-61-2023 mailto: p.yamin[at]fz-juelich.de

Re: [gmx-users] Double vs. Charged Single bonded Oxygen in GROMOS96.1

On Monday 27 October 2008 18:08, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > Hi again dears, > > > > I should ask for another comment. I have a Phorphorus to which two Oxygen > > atoms are bonded. One O is double bonded and the other has only a single > > bo

[gmx-users] Double vs. Charged Single bonded Oxygen in GROMOS96.1

. both have the same charge (-0.421) and mass (15.9994). I guess the charge is reasonable for the double-bonded one, but not for the one with a single bond and a free electron. How could I correct this? Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen

Re: [gmx-users] Adding Na ions to DPPG

On Monday 27 October 2008 15:12, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > On Monday 27 October 2008 14:08, Mark Abraham wrote: > >> Peyman Yamin wrote: > >>> Dear GMX users, > >>> > >>> I want to add sodium ions (Na+) to a phos

Re: [gmx-users] Adding Na ions to DPPG

On Monday 27 October 2008 15:07, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: > > > > Actually I'm doing a funny mistake telling I should replace an O with an > > Na! (probably because of high adre

Re: [gmx-users] Adding Na ions to DPPG

one O has no H and thus is negative. an Na+ should accompany this O. > Peyman Yamin wrote: > > Dear GMX users, > > > > I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the > > structure with the Na replaced with O. I get a .top with this from prodrg >

Re: [gmx-users] Adding Na ions to DPPG

On Monday 27 October 2008 14:08, Mark Abraham wrote: > Peyman Yamin wrote: > > Dear GMX users, > > > > I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the > > structure with the Na replaced with O. > > That doesn't make sense to me. > >

Re: [gmx-users] Adding Na ions to DPPG

rionic DPPG has always its Na+ beside its O-. On Monday 27 October 2008 14:03, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > Dear GMX users, > > > > I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the > > structure with the Na replaced with O. I g

[gmx-users] Adding Na ions to DPPG

d Cheers, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromac

Re: [gmx-users] g_sas, what's it all about?

On Thursday 31 July 2008 13:34, Justin A. Lemkul wrote: > Peyman Yamin wrote: > > On Wednesday 30 July 2008 12:58, David van der Spoel wrote: > >> Peyman Yamin wrote: > >> > Hello List! > >> > > >> > > >> > > >&

Re: [gmx-users] g_sas, what's it all about?

On Wednesday 30 July 2008 12:58, David van der Spoel wrote: > Peyman Yamin wrote: > > Hello List! > > > > I use g_sas to calculate the solvent accessible surface area of some > > amphiphiles. g_sas gives the result as hydrophobic area! I'm wondering if > &g

[gmx-users] g_sas, what's it all about?

empirical science were the only kind of science possible. -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [EMAIL PROTECTED] ___ gmx-users ma

Re: [gmx-users] doesn't match coordinate file with topology

le. in [ molecules ] part of the topology the number of the molecules should be mentioned correctly. if you delete things from coordinate file, you should apply the proper change to the topology as well. it seems you have more atoms in your gro than what is expected from the topology file. might wa

[gmx-users] How to build boxes with constant number of solvent molecules?

crash. Does one know any practical strategy to solvate a molecule in a box and have the number of solvent molecules fixed?? I appreciate any suggestions, regards, Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen

Re: [gmx-users] minimisation and constraints

e have to set "constraints = none"? > > I just don't remember where I saw something like this. Any comment here > would be very appreciate. > > Many thanks in advance, > > Alan -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik University

Re: [gmx-users] centering molecule in the water box

ease 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 -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr

Re: [gmx-users] Error with polymer surface modeling

m types to the ffG43a1nb.itp and ffG43a1bon.itp > ? But then where should I get different parameters. > > Thank you for your help. > > Harshith Asuri, > 3rd year UG student > IIT Kanpur, > http://home.iitk.ac.in/~harshith -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrens

Re: [gmx-users] centering molecule in the water box

man/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] bicelle gromacs MD simulation CG model?

oefficients derived from Octanol-Water systems and say it's the same for a Phospholipid-Water system. Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 913

Re: [gmx-users] analysis of different groups with g_energy

On Tuesday 10 June 2008 16:07, Mark Abraham wrote: > Peyman Yamin wrote: > > Good day! > > > > Thanks for the comments, but maybe it could be done in a less laborious > > way as following? > > > > g_energy gives all the interactions between MOL and SOL othe

Re: [gmx-users] g_density problem segmentation fault glibc detected

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? R

Re: [gmx-users] secondary structure

> NCE in Physical Chemistry, > University of Peshawar. > NWFP,Pakistan. > Cell # 03349060632. > > Send instant messages to your online friends http://uk.messenger.yahoo.com -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Er

Re: [gmx-users] analysis of different groups with g_energy

above (at least with a reasonably small error). If it's not supposed to work from the beginning, i.e. the terms are not additive at all, please let me know! as well as if one should add/substract some things! Peyman On Tuesday 10 June 2008 03:40, Mark Abraham wrote: > Peyman Yamin w

Re: [gmx-users] analysis of different groups with g_energy

d add together from? I think I'd need all bonding and nonbonding interactions! or I should even calculate them? I can't also find what SR and LR and 14 mean in energy terms...! Would greatly appreciate any suggestion, Peyman On Monday 09 June 2008 18:27, Mark Abraham wrote: >

Re: [gmx-users] analysis of different groups with g_energy

June 2008 18:27, Mark Abraham wrote: > Peyman Yamin wrote: > > On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: > > > > Well, ofcourse I did! otherwise I wouldn't expect any program to know > > them by itself! the problem is that I say: > > Well, there&#x

Re: [gmx-users] analysis of different groups with g_energy

file. > > -Justin > > Peyman Yamin wrote: > > Dear Gromacs users, > > > > I'm simulating dilute solutions of different surfactants in different > > media. All I want to analyse afterwards, though, is the single surfactant > > molecule properties! > >

[gmx-users] analysis of different groups with g_energy

at command-line, that I want, say total-energy of group G! Thanks in advance, Best regards Peyman -- Peyman Yamin Lehrstuhl fuer Thermische Verfahrenstechnik Universitaet Erlangen-Nuernberg Egerlandstr. 3 91058 Erlangen Phone: +49(0) - 9131 - 85 27671 Mailto: [

[gmx-users] Simulation of ordered molecular structures

Dear gromacs users, I'm trying to simulate amphiphilic molecules, building stable structures by non-bonded interactions. I have seen in biological research, membranes and proteins therein are often subject of simulations. A cell membrane, I guess, could be an example of a structure built not by