[gmx-users] Re: gmx-users Digest, Vol 83, Issue 160

2011-03-26 Thread Kishore
Dear Mark, As you correctly pointed out, I had looked into those improper dihedral specifications several times before and it seems that they are properly mentioned in the .itp file. I have been using the topologies generated by PRODRG server for NADPH as i could not make it comply with the inbuil

Re: [gmx-users] Re: Alcohol Dehydrogenase MD simulation....Reg

2011-03-26 Thread Justin A. Lemkul
Please choose a relevant subject line and do not reply to the entire digest; it confuses the archive. Kishore wrote: Dear Mark, As you correctly pointed out, I had looked into those improper dihedral specifications several times before and it seems that they are properly mentioned in the .

[gmx-users] mdrun cannot append to file larger than 2Gb

2011-03-26 Thread Warren Gallin
Hi, Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got an error that I have never seen before, to whit: Program mdrun_mpi, VERSION 4.5.3 Source code file: /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: 1727 Fatal error: The original run wro

Re: [gmx-users] mdrun cannot append to file larger than 2Gb

2011-03-26 Thread Justin A. Lemkul
Warren Gallin wrote: Hi, Using GROMACS 4.5.3 I tried to continue an mdrun from a checkpoint, and got an error that I have never seen before, to whit: Program mdrun_mpi, VERSION 4.5.3 Source code file: /global/software/build/gromacs-4.5.3/gromacs/src/gmxlib/checkpoint.c, line: 1727 Fatal er

[gmx-users] Best Program for Simulating Lipid Bilayers in Water

2011-03-26 Thread Nancy
Hi All, I heard that LAMMPS is supposedly good for simulating lipid bilayers in water. I haven't used LAMMPS before; does anyone know if it would be worth to try it in addition to Gromacs? Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

Re: [gmx-users] Re: Alcohol Dehydrogenase MD simulation....Reg

2011-03-26 Thread Mark Abraham
Kishore wrote: Dear Mark, As you correctly pointed out, I had looked into those improper dihedral specifications several times before and it seems that they are properly mentioned in the .itp file. I have been using the topologies generated by PRODRG server for NADPH as i could not make i

[gmx-users] RMSD Calculation

2011-03-26 Thread Nancy
Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. Thank you very much, Nancy -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] RMSD Calculation

2011-03-26 Thread Justin A. Lemkul
Nancy wrote: Hi All, I need to determine the RMSD of a small molecule cocrystallized ligand, against a large number of predicted docked conformations. Please let me know what is the best method for doing this. I answered this yesterday: http://lists.gromacs.org/pipermail/gmx-users/2011

[gmx-users] How can I convert Gromacs ouput to Desmond input file??

2011-03-26 Thread 김현식
Dear experts, Hi, I used to gromacs for MD, but there is need to make desmond file from gromacs output. If there is anyone who know how to this, please let me know. Thank you very much. -Hyun--- gmx-users mailing listgmx-users@gro

Re: [gmx-users] How can I convert Gromacs ouput to Desmond input file??

2011-03-26 Thread Mark Abraham
On 27/03/11, 김현식 wrote: > > > > > > > > > Dear experts, >   > Hi, I used to gromacs for MD, but there is need to make desmond file from > gromacs output. > > > > > > > > When linked against an installation of VMD, GROMACS can read and write any file format that VMD can do. Fo

[gmx-users] heat capacity in 4.5.3 and 4.0.7

2011-03-26 Thread Elisabeth
Dear all, I am trying to calculate Cv of a pure alkane 125 molecules with actual density, and here is what I have done: 1- Cv: Run NVT > g_energy>select T and Etot=total energy As I issue g_energy *.edr Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000369503) And when I choose –nmol

[gmx-users] make_ndx

2011-03-26 Thread ZHAO Lina
Hi, Does the "!" in make_ndx work? "|" and "&" work, but seems "!" not work. I met something weird, suppose I choose a C11, which is from ri 1-111. if use a C11, the atom is 111 if use a C11 & ri 1-111, the atom is 111 if use a C11 & ri 101-111, the atom is 5. Which is expected to be 10, so this

[gmx-users] Re: make_ndx

2011-03-26 Thread ZHAO Lina
such as residue 288 which is has C when I tried a C, it's inclusive residue 288. while tried the ri 288 & a C, it showed me Group is empty. Thanks, On Sun, Mar 27, 2011 at 1:42 PM, ZHAO Lina wrote: > Hi, > > Does the "!" in make_ndx work? > > "|" and "&" work, but seems "!" not work. > > I met

[gmx-users] amide partial charges

2011-03-26 Thread XUEMING TANG
Hi May I ask if anyone know a good reference for partial charges of "-CH2-NH-CO-CH2-CH2"(amide)? I plan to use gromos 53A6 force field. I searched the internet quite a while but not sure what is the best. I will be appreciated if you could recommend one with the reference paper. Thank you in advan

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 188

2011-03-26 Thread Kishore
(un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > > > Justin A. Lemku