Re: [gmx-users] Light-controlled MD

Chih-Ying Lin wrote: HI Some surfactants can be light-controlled. Could anyone directed me how to simulate the light-controlled surfactants system with MD? I would think the answer to your question is "no". Classical force fields are not suited to such systems. Mark _

Re: [gmx-users] Gromacs 4.0.3 released

Hi All, Wasn't support for CHARMM27 supposed to be included in this release? I thought there had been a few discussions about it over gmx-developers regarding the CVS code, which I haven't checked out in a while. I also see, for example, #ifdef _FF_CHARMM in spc.itp, tip3p.itp, etc, but ther

Re: [gmx-users] How to determine if it is the pi-pi stacking interaction?

Chih-Ying Lin wrote: Hi How to determine if it is the pi-pi stacking interaction? Visual inspection, g_mindist, g_mdmat, and g_dist might be useful, along with reading through the manual for descriptions of the analysis tools while searching for relevant terms. -Justin My system are

[gmx-users] How to determine if it is the pi-pi stacking interaction?

Hi How to determine if it is the pi-pi stacking interaction? My system are surfactants mixing with water. The surfactants carries phenyl-groups. Thanks Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

[gmx-users] Light-controlled MD

HI Some surfactants can be light-controlled. Could anyone directed me how to simulate the light-controlled surfactants system with MD? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Pl

[gmx-users] Gromacs 4.0.3 released

Hi everybody, We've just released a maintenance version 4.0.3 with a bunch of bugfixes and minor enhancements - all issues in bugzilla that had been settled to be bugs have been fixed. You can find it in the usual place: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.0.3.tar.gz Some of the f

RE: [gmx-users] Inconsistent shifts Problem when using g_rdf

Problem is solved. Thanks, Po-Han Date: Fri, 16 Jan 2009 09:31:28 +0100 From: Berk Hess Subject: RE: [gmx-users] Inconsistent shifts Problem when using g_rdf To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="windows-1252" > Date: Fri, 16 Jan 2009 09:06:43

Re: [gmx-users] wrong format in input file ffamber03.hdb on line

drugdesign wrote: Dear Gromacs users, I am getting and eeror while loading Amber03 force field by pdb2gmx command: --- Program pdb2gmx, VERSION 4.0.2 Source code file: h_db.c, line: 87 Fatal error: wrong format in input file ffamber03.hdb on

Re: [gmx-users] Where can I get .gro and .itp files for different models of water?

drugdesign wrote: Dear Gromacs users, I am making tutorial on GROMACS but I can't find mdcourse folder in my installed software. I've taken spc.gro from spc.pdb from tutor folder. I wonder where can I get spc.itp and spc216.gro? In tutorial it is reffered to mdcourse directory, but I don't hav

Re: [gmx-users] environment variable GMX_MAXCONSTRWARN to -1,

drugdesign wrote: gmx-users@gromacs.org Dear Gromacs users, I've got an error while runing molecular dynamics simulation in GROMACs. Where can I find GMX_MAXCONSTRWARN and where can I set it? Program mdrun, VERSION 4.0.2 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warni

[gmx-users] Where can I get .gro and .itp files for different models of water?

Dear Gromacs users, I am making tutorial on GROMACS but I can't find mdcourse folder in my installed software. I've taken spc.gro from spc.pdb from tutor folder. I wonder where can I get spc.itp and spc216.gro? In tutorial it is reffered to mdcourse directory, but I don't have such a directory. I

[gmx-users] wrong format in input file ffamber03.hdb on line

Dear Gromacs users, I am getting and eeror while loading Amber03 force field by pdb2gmx command: --- Program pdb2gmx, VERSION 4.0.2 Source code file: h_db.c, line: 87 Fatal error: wrong format in input file ffamber03.hdb on line 2

[gmx-users] environment variable GMX_MAXCONSTRWARN to -1,

gmx-users@gromacs.org Dear Gromacs users, I've got an error while runing molecular dynamics simulation in GROMACs. Where can I find GMX_MAXCONSTRWARN and where can I set it? Program mdrun, VERSION 4.0.2 Source code file: constr.c, line: 136 Fatal error: Too many LINCS warnings (2483) If you know

Re: [gmx-users] Thank you

Sunil Thapa wrote: Respectable Mark Thank you very much for your immediate response. I have added new atom type in the ffgmx.atp file and also modified ffgmx.itp, ffgmxnb.itp. After that the pdb2gmx worked. I used genbox to add water in the oxygen molecule system. For now I have taken only 2 o