[gmx-users] how to search in the new GROMACS website ?

Dear GMX-users, In the old website, I was able to search any topics (questions or answers) by simply typing key words. But, it looks like, in the new website, I need to open each archives for each year and month. Is there any way that I can search more easily? Would you please tell me h

Re: [gmx-users] C6 constant units

* Vitaly V. Chaban [2009-06-26 23:31:38 +0300]: Hi, In what units C6 constants are present in the force field files? Hm [ C6/r^6 ] should yield an energy unit, so perhaps kJ * nm^6 / mol ?? However the C6 constants in the force field fields correspond to different parameters of the LJ po

[gmx-users] Dihedral functions

What are the exact functional forms for the three dihedral type functions (listed on page 90 of the GROMACS Manual). I might have them figured out, but I can't find anything that confirms that I do. _ MSN 메신저의 차세대 버전, Windows Live

[gmx-users] C6 constant units

Hi, In what units C6 constants are present in the force field files? Thank you, Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search bef

Re: [gmx-users] 45a4 force field files to nucleic acids simulations

PERFECT!! Thanks Tsjerk!! Best wishes!! 2009/6/26 Tsjerk Wassenaar > Hi Guilherme, > > These parameters are kept in the later series 53a5 and 53a6. > > Cheers, > > Tsjerk > > On Fri, Jun 26, 2009 at 7:19 PM, Guilherme Menegon > Giesel wrote: > > Hello folks!!! > > > > I'm trying make simulation

Re: [gmx-users] pdb2gmx fatal error

Dave Hassan wrote: Hi, I'm trying to run a simple simulation of a DNA hairpin pdb entry 1pqt. When I run pdb2gmx with the G43a1 force field I get the error: Warning: 'DG' not found in residue topology database, trying to use 'DGUA' --- Pro

[gmx-users] pdb2gmx fatal error

Hi, I'm trying to run a simple simulation of a DNA hairpin pdb entry 1pqt. When I run pdb2gmx with the G43a1 force field I get the error: Warning: 'DG' not found in residue topology database, trying to use 'DGUA' --- Program pdb2gmx, VERSION 4

Re: [gmx-users] 45a4 force field files to nucleic acids simulations

Hi Guilherme, These parameters are kept in the later series 53a5 and 53a6. Cheers, Tsjerk On Fri, Jun 26, 2009 at 7:19 PM, Guilherme Menegon Giesel wrote: > Hello folks!!! > > I'm trying make simulations with nucleic acids with GROMOS. I know that was > published the article " An improved nucle

Re: [gmx-users] simulation of protein in presence of ATP

Independently of your ATP position, your system may explode or show LINCS warnings if you use pressure and temperature coupling. I had these problem, and corrected it removing the pressure coupling. Pressure coupling will let your system expand in response to the heat, and if the positions are

[gmx-users] 45a4 force field files to nucleic acids simulations

Hello folks!!! I'm trying make simulations with nucleic acids with GROMOS. I know that was published the article " An improved nucleic acid parameter set for the GROMOS force field", showing new parameters to describe nucleic acids conformations. Such parameters was inserted in a new force field:

[gmx-users] file conversion from Amber to GROMACS for protein-ligand complexes

Dear GROMACs users, we have a task to use Amber force fields for protein-ligand complexes for GROMACS MD simulation. Which strategy is better to use? 1. To make .inpcrd and .prmtop files and then apply amb2gmx.pl script. Is output for the protein-ligand complex for this script will be correct?

[gmx-users] g_dist: Indexfile seem to be NOT optional

Hi GMXers, according to the man page of g_dist, the -n option is optional. But when I try to use g_dist without -n (and without an index.ndx in the working directory), I get the following error: --- Program g_dist, VERSION 4.0.5 Source code file

Re: [gmx-users] Re: Ligand & Receptor

This is neat! Thanks http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs On Fri, Jun 26, 2009 at 9:36 AM, Alan wrote: > Hi there, > How about taking a look at acpypi.googlecode.com and its wikis? > I hope it can help you. > Alan > On Fri, Jun 26, 2009 at 14:27, wrote: >> >> Hello, >> >> I

[gmx-users] Re: Ligand & Receptor

Hi there, How about taking a look at acpypi.googlecode.com and its wikis? I hope it can help you. Alan On Fri, Jun 26, 2009 at 14:27, wrote: > > Hello, > > I'm trying to figure out how I can merge the ligand and receptor > files. I used this script to prep a ligand I treated with GAFF > > perl

Re: [gmx-users] Ligand & Receptor

Jack Shultz wrote: Hello, I'm trying to figure out how I can merge the ligand and receptor files. I used this script to prep a ligand I treated with GAFF perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand This results in ligand.top & ligand.gro Then I prepped a recept

[gmx-users] Ligand & Receptor

Hello, I'm trying to figure out how I can merge the ligand and receptor files. I used this script to prep a ligand I treated with GAFF perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand This results in ligand.top & ligand.gro Then I prepped a receptor pdb2gmx_d -f fzd2.p

Re: [gmx-users] mdrun -c option "did not work"

Jérôme Baffreau wrote: Thanks for your answer. Actually no my run did not finish normally the first time (it has been stopped after 7 days because of the time limitation on the cluster it was running on). So I started it again (I ran the same command and added the option "-append yes") and

Re: [gmx-users] grommp errors

wuxiao wrote: > Dear gmx users, While I am running grompp, many errors are identified as > follows: Error 124 [file **.top, line ] No default Ryckaert-Bell types > What happened to this? How to cope with this problem? You have specified an R-B dihedral for which no parameters exist. You'll

[gmx-users] grommp errors

Dear gmx users, While I am running grompp, many errors are identified as follows: Error 124 [file **.top, line ] No default Ryckaert-Bell types What happened to this? How to cope with this problem? Any reply would be acknowledged very much. Sincerely Chaofu Wu