[gmx-users] The problem of .trr file size limit?

Hello, everyone I submit a job with gromacs-4.5.4 in cluster ,but the md.trr file can not write if the file size more than 17247,252,480K(about 16.06G)? and the program always output :Cannot write trajectory frame; maybe you are out of quota? There is sufficient disk space,and the

[gmx-users] %hbond number problem

Dear Justin I download the script plot_hbmap.pl and input perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n, but the output info is Unrecognized switch: -bash (-h will show valid options).; then,I input perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n,and

[gmx-users] %hbond number problem

Dear Justin I download the script plot_hbmap.pl and input perl $0 -s b4md.pdb -map hbmap.xpm -index hbond.ndx\n, but the output info is Unrecognized switch: -bash (-h will show valid options).; then,I input perl\n plot_hbmap.pl -s b4md.pdb -map hbmap.xpm -index

[gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?

Dear all I want to count all of the hydrogen bond's lifetime and donor-acceptor atoms in simulation,but I don't know how to do it. In many papers,the hydrogen bonds are list in this form: Donor Acceptor %Exist. ARG58

[gmx-users] How to countting Hbonds lifetime

Hi Erik and Justin Thanks for your reply. I want to obtain the HBond's permanence time.May be it's occupancies that you said. So,could you send me the script? Thank you very much. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Re: How to countting Hbonds lifetime

Hi Justin What is your means that the HBond's occupancy ? Can you tell me the difference about Hbonds lifetime and occupancy? I want to know which residues form the Hbond and the donor-acceptor atoms. The g_hbond can do it? Thank you very much. -- gmx-users mailing list

[gmx-users] ffamber03 RB dihedrals and amb2gmx.pl problem!

Hello all I obtained a top file after running the amb2gmx.pl script,but I feel some errors in this top file. The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo presence in it. And the manual is point that with the Ryckaert-Bellemans potential the 1-4 interactions

[gmx-users] Re:gmx-users Digest, Vol 82, Issue 168

Hi all, If anyone have a script that amb2gmx_dihe.pl provide by Guillem Portella,could you send me a copy? Thanks very much!-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] ffamber03 RB dihedrals and amb2gmx.pl problem!

Hello all I obtained a top file after running the amb2gmx.pl script,but I feel some errors in this top file. The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo presence in it. And the manual is point that with the Ryckaert-Bellemans potential the 1-4 interactions

[gmx-users] ffamber03 top file problem

Dear All: I want to obtain a top file for protein with ffamber03 force field,and correct some bonds and angles parameter. I added a new atom type HD(D2O) in ffamber03 [ atomtypes ], so I added some HD parameters in ffbond.itp、atomtypes.atp and ffnonbond.itp files,the output of the program

[gmx-users] topolbuild1_3 install problem

Hi, Mark, Thanks for the reply. You'are right,I forgot to enter the path.And my computer system is Ubuntu 10.04.I want to use the glycam force filed, then I type the command: software/topolbuild1_3/src/topolbuild -h I got the correct help information. But when I type this integral

[gmx-users] glycam force field problem

Hi OliverI'm sorry to reply you so later.And I have some questions after reading your letter.You said that “The fudgeLJ under defaults should be 1.0 for GLYCAM“ and ”When you run grompp check in theoutput that fudge is set to 1.0.” Do you means to setting the fudgeLJ value to 1.0 in em.tpr

[gmx-users] topolbuild1_3 install problem

Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I

[gmx-users] topolbuild1_3 install problem

Hi all I downloaded topolbuild1_3 from the GROMACS website, and I run the command as follows: path: home/buct/topolbuild1_3 ” # tar -xvf topolbuild1_3.tgz #make -f Makefile ; (intel CPU) there were no any error messages. then I

[gmx-users] Re:gmx-users Digest, Vol 80, Issue 164

Hi Alan , Oliver I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct , because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not. Would you give me some advice?

[gmx-users] amb2gmx.pl file

Hi Alan , Oliver I have obtained the gromacs format files by amb2gmx.pl script, but I am not sure if this flies are correct , because all of the [pairs](1-4 interaction) are zero in gromacs top files. I don't know whether this files are correct or not. Would you give me some advice?

[gmx-users] amber convert gromacs input files

Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format. Can anyone help me to convert this (amber) files to gromacs input files(top or