Re: [gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format

On Jan 17, 2013, at 12:27 , Justin Lemkul wrote: > > > On 1/17/13 6:22 AM, Anna Marabotti wrote: >> Dear all, >> we'd need to convert a trajectory in .xtc format (and the related topology >> file) >> to a format that could be read by Amber program (I'd need to perform MM-PBSA >> calculations).

Re: [gmx-users] RE: vsite problem in gromacs 4.0

On Nov 6, 2008, at 17:45 , Daniel Larsson wrote: On Nov 6, 2008, at 14:48 , Berk Hess wrote: Hi, I fixed the virtual site charge group issue in mdrun for 4.0.1. Now vsite aromatics will run fine. But there is still an issue in pdb2gmx for some proteins when selecting the OPLS force field

Re: [gmx-users] RE: vsite problem in gromacs 4.0

On Nov 6, 2008, at 14:48 , Berk Hess wrote: Hi, I fixed the virtual site charge group issue in mdrun for 4.0.1. Now vsite aromatics will run fine. But there is still an issue in pdb2gmx for some proteins when selecting the OPLS force field. I hope we can fix this for 4.0.1. Is it something

Re: [gmx-users] problem with openmpi and gromacs4.0

On Nov 6, 2008, at 15:04 , hui sun wrote: Dear all, Recently, we installed the gromacs4.0 with openmpi parallel program. When we started a simulation with np=1, the simulation was finished normally. But when the same tpr file was run with np=n (n>1), I obtained the following error messag

Re: [gmx-users] continuation options

On Nov 11, 2008, at 15:39 , Berk Hess wrote: > With Gromacs 4.0 I get this message: > > NOTE: The simulation uses pressure coupling and/or stochastic dynamics. > tpbconv can not provide binary identical continuation. > If you want that, supply a checkpoint file to mdrun > > Is it possible to

[gmx-users] continuation options

With Gromacs 4.0 I get this message: NOTE: The simulation uses pressure coupling and/or stochastic dynamics. tpbconv can not provide binary identical continuation. If you want that, supply a checkpoint file to mdrun Is it possible to extend a trajectory with mdrun, a checkpoint file and a new

Re: [gmx-users] problem with center of mass removal, rest-group, all gmx versions

On Dec 10, 2008, at 7:45 , Michael Brunsteiner wrote: In ALL my md.log files is see the following output: We have the following groups for center of mass motion removal: 0: rest, initial mass: 163113 There are: 6508 Atoms in the mdp-documentation it says: comm_grps: group(s) for center

Re: [gmx-users] problem about position restrain

nterface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala University +46-18-471 4006 (phone) +46-18-511 755 (f

[gmx-users] PME grid parameters in large system run in parallel in Gromacs 4 CVS

after a long time in the queue due to an incompatible number of nodes. A feature of mdrun would be to choose not to use x number of nodes if it would improve performance rather than just die.) --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala

Re: [gmx-users] peptide MD

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 --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala University +46-18-471 4006 (phone)

Re: [gmx-users] constraints & cg

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 --- Daniel Larsson Molecular Biophysics group Department

Re: [gmx-users] Data generated by g_sas

PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala University +46-18-471 4006 (phone) +46-18-511 755 (fax) http://xray.bmc.uu.se/~larsson [

Re: [gmx-users] how to make choices of COM in the system with freeze group?

he list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala University +46-18-471 4006 (phone) +46-18-511 755 (fax) http://xray.

Re: [gmx-users] NVT simulation

. Settings should be made in the .mdp file. Refer to the manual, the tutorial and material on the Gromacs homepage to learn more about the fundamental parts of performing simulations. - Daniel --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala

Re: [gmx-users] ngmx crash

e www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala University +46-18-471 4006 (phone) +46-18-511 755 (fax) http://xray.bmc.uu.se/~lars

Re: [gmx-users] how to neutralise: Non-integer charges

chive 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 --- Daniel Larsson Molecular Biophysics group Departm

Re: [gmx-users] chirality check

Read http://www.gromacs.org/mailing_lists/users.php --- Daniel Larsson Molecular Biophysics group Department of Cell and Molecular Biology Uppsala University +46-18-471 4006 (phone) +46-18-511 755 (fax) http://xray.bmc.uu.se/~larsson [EMAIL PROTECTED] _

Re: [gmx-users] b-factor

On Oct 22, 2007, at 10:07, tangxuan wrote: Dear all, I have got a pdb file by command g_rmsf and option -oq, and the content of the file is like this: TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 148.918 148.918 148.428 59.89 59.89 90.00 P 1 1 MODEL