Re: [gmx-users] Forces are large - How to track down the culprit

>> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> _______ >> gmx-users mailing listgmx-users@gromacs.org >> http://www.gromacs.o

Re: [gmx-users] Problems with parallelisation of GROMACS on a Mac Pro (OS X)

lt is the same for GROMACS 3.3.1, 3.3.3 and the recent CVS. Does anybody have a suggestion? Is the problem more related to LAM then to GROMACS? Greetings Steffen -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/6

Re: [gmx-users] Analysis of mutants

ds to use. Also, I think it is better to get some help from people who have done this type of analysis many times. I am waiting for your reply. Thank you -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 B

Re: [gmx-users] cholesterol distortion

n't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] We

Re: [gmx-users] Black whole simluations

Hello Ben, aehm, is it already the 1st of April? That's the traditional day in Germany to make fun of others. In case this is a serious request, let's get this straight: GROMACS is a program for biomolecular simulations. NOT for astronomic systems. In addition I'd have problems to interpret your r

Re: [gmx-users] information for analysis

s.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://ww

Re: [gmx-users] make_hole error installation

aving directory `/usr/local/gromacs-3.3.2/src/gmxlib' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/usr/local/gromacs-3.3.2/src' > make[1]: *** [all] Error 2 > make[1]: Leaving directory `/usr/local/gromacs-3.3.2/src' > make: *** [all-recursive]

Re: [gmx-users] Gel Phase in DMPC using Berger force field ??

is the Berger > force field not parametrized to reproduce the gel phase at all? > > Thanks at lot, > Jochen > > -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +

Re: [gmx-users] b-factor

ting! > 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 > -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department

Re: [gmx-users] How Long to Equlibrate?

sting! > 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 -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysic

Re: [gmx-users] N-glycosylation of a protein

quests 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 -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germ

Re: [gmx-users] GROMOS96 and POPE

_ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] > Can't post? Read

Re: [gmx-users] Gromacs 96 and POPE

agline > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [EMAIL PROTECTED] &

Re: [gmx-users] water molecules in vacuum simulation.

on'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 > -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany

Re: [gmx-users] position restraints crashing

ch minimization algorithm did you use? Steep or CG? -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de __

Re: [gmx-users] position restraints crashing

_ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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

Re: [gmx-users] POPC simulation

mx2nb.itp and ffgmx2bon.itp explicitly? They are already set up by calling ffgmx.itp in the beginning, you're just overriding everything again. So: after modifying lipid.itp, you should do fine with #include "ffgmx.itp" #include "popc.itp" Bye Steffen -- Dipl.-Chem. Steffen

Re: [gmx-users] POPC simulation

gs Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de ___ gmx-users mailing listg

Re: [gmx-users] Topology question

Hi Anthony, search for a mail by christian burisch on this topic, posted on the list yesterday... -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.

Re: [gmx-users] ffG43a2x and ffgmx dppc.itp file

er reliable one. cheers Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] Req for script to make rtp entro of ligand with ffoplsa compatiable

Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the lis

Re: [gmx-users] Protein out of water box

tp://www.gromacs.org/mailing_lists/users.php Hi Gajula, maybe a stupid question, but: is your simulation box larger than the protein itself, as it has to be? Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67

Re: [gmx-users] Re: LINCS Warning using mdrun

l existing. Did you check which where the atoms mentioned by the lincs warning or if there were bad angles or contacts in the starting structure? -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany _

Re: [gmx-users] LINCS Warning using mdrun

Hi Gaurav, what is your stepsize during the simulation? what is constrained? And have you run a minimization before starting the simulation? hear from you soon Steffen -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67