[gmx-users] about the option pull_dim

Dear all, Does the following three options do the same things in the pull code of Gromacs 4.0: 1. pull_dim = Y Y Y pull_vec1 = 1 0 0 ** 2. pull_dim = Y N N pull_vec1 = 1 0 0 ** 3. pull_dim = Y N N pull_vec1 = 1 0.5 0.5 -- gmx-users

[gmx-users] Lysozyme benchmarking for gromacs-4,0.5

Hi there, I am running a GROMACS benchmarking on my cluster with the Lysozyme example provided in benchmarking files. I am looking at ns/day to compare the performance of various runs. I am using gromacs-4.0.5, Can somebody provide me with the figures to compare the performance? Also DO I need to

Re: [gmx-users] Lysozyme benchmarking for gromacs-4,0.5

- Original Message - From: vivek sharma viveksharma.i...@gmail.com Date: Wednesday, August 25, 2010 16:48 Subject: [gmx-users] Lysozyme benchmarking for gromacs-4,0.5 To: Discussion list for GROMACS users gmx-users@gromacs.org Hi there, I am running a GROMACS benchmarking on my

Re: [gmx-users] VDW radii of Br and K+

On 2010-08-24 22.53, nishap.pa...@utoronto.ca wrote: Hello, I converted a .tpr file for Bromine ion and Potassium ion using -mead option and editconf. It gives out the Van der Waals radius of the atom, but I don't understand why i got ~2.46A for Potassium and ~2.31A for Bromide. Isn't the

[gmx-users] Installating GROMACS with MPI

Hi, I am installing GROMACS with the mpi option. There is some problem with the flags of pgcc. The version of pgcc is pgcc 7.0-5 64-bit target on x86-64 Linux. and that of gromacs gromacs-4.5-beta2. I can remove the flags by hand but I dont know if this procedure will modify the performance of

Re: [gmx-users] Installating GROMACS with MPI

- Original Message - From: poj...@icp.uni-stuttgart.de Date: Wednesday, August 25, 2010 19:16 Subject: [gmx-users] Installating GROMACS with MPI To: gmx-users@gromacs.org Hi, I am installing GROMACS with the mpi option. There is some problem with the flags of pgcc. The version of

Re: [gmx-users] about the option pull_dim

DeChang Li wrote: Dear all, Does the following three options do the same things in the pull code of Gromacs 4.0: No, but without further context, it's hard to tell you what each set is doing. Most notably, the choice of *either* pull_dim or pull_vec1 will be motivated by the

RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi, I fixed all the terminal residue issues. The automatic HIE terminal translation is still swtiched by the env.var. I'm still thinking if there could be issues when we turn that always on. Berk From: alanwil...@gmail.com Date: Tue, 24 Aug 2010 22:55:57 +0100 Subject: Re: [gmx-users] pdb2gmx

RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi, I now turned on the automatic HIE, and analogous, terminal renaming on by default. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now Date: Wed, 25 Aug 2010 14:34:30 +0200 Hi, I fixed all the terminal

Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Just one more question. How are you handling CYS? In amber it could be CYP, CYN etc. Thanks a lot, Alan On 25 August 2010 13:59, Berk Hess g...@hotmail.com wrote: Hi, I now turned on the automatic HIE, and analogous, terminal renaming on by default. Berk

RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

You can find the residue name to rtp translation table in: share/top/amber99.ff/aminoacids.r2b I don't have a list with Amber names and funtions for the amino acids. Currently for Amber in Gromacs we have CYS (standard, neutral, protonated) and CYX (disulfide bond). Does Amber use CYP instead of

[gmx-users] g_mdmat

Dear friends, I have used g_mdmat g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg I got dm.xpm graph which shows mean of whole simulation residue contacts. How to get information about the particular residue are n contact? I mean to say, Is there any tool to give list of

Re: [gmx-users] pbc atom

Dear Chris and Justin I ran a simulation for two water molecules (100 ns). It only took 5 minutes. Firstly I ran the simulation with ref distance 2.35 nm, genvel =yes, and gen temp =600 (using Nose Hoover). This produced a histogram with one main peak. I then took the final configuration from

RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi, I just found that normal cysteine in Amber is CYS. I think all Amber rtp entries now conform to the Amber nomenclature. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now Date: Wed, 25 Aug 2010 15:36:16 +0200

Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Not really, I mentioned that based on Sorin's ffamber page: a) Non-terminal amino and nucleic acid residues follow standard AMBER naming conventions. To avoid confusion between GROMACS and AMBER conventions, we have omitted the redundant HIS residue, leaving HID, HIE, HIP, and terminal versions

Re: [gmx-users] VDW radii of Br and K+

Thanks! I did overlook that. Quoting David van der Spoel sp...@xray.bmc.uu.se: On 2010-08-24 22.53, nishap.pa...@utoronto.ca wrote: Hello, I converted a .tpr file for Bromine ion and Potassium ion using -mead option and editconf. It gives out the Van der Waals radius of the atom, but I

RE: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Hi, This is completely unrelated. Eric changed all the names to allow processing of his ports by Gromacs version 3.3 and 4.0. In 4.5 I enabled fully rtp name flexibility and I changed all rtp names back to the Amber nomenclature. Berk From: alanwil...@gmail.com Date: Wed, 25 Aug 2010

Re: [gmx-users] pdb2gmx e82fc gmx 4.5 is failing with DNA now

Ah, great. Thanks Berk. FYI, because I am developing a tool (ACPYPE) and I wrote the test using gromacs and ff oplsaa and amber so that's why it's relatively easy and quick to test and check the issues I was having. But it also happens that I am adapting my test code for gmx 4.5 and so I bump in

[gmx-users] dihedral function type 9 in rtp file

Hi, In the rtp file of Gromacs version 4.5-beta3, the dihedral function type for proper dihedrals is 9. However, I can't find any documentation about the function form of this function type. Also, you can add multiple dihedral potentials for one dihedral term explicitly in the rtp file. The term

[gmx-users] How to tell if the molecule is correctly reduced?

Hi I did simulations for a protein with disulfide bonds using opls. Then I reduced the ssbonds in vmd and did simulations for the reduced. When loading gro(or pdb) and trr files on vmd I do not see reduced bonds. I also compared the two pdb files and they looked the same in terms of number of

Re: [gmx-users] How to tell if the molecule is correctly reduced?

Hi, if the gro file written by pdb2gmx contains the same number of hydrogens then before, than you disulfide bonds haven't changed. pdb2gmx automatically forms disulfide bridges if the atoms are within some distance (see specbond). Look at the output of pdb2gmx and make sure it is doing what you

[gmx-users] initial velocities analysis

Dear gmx-users, sorry for my trivial questions, but I didn't find an answer searching in the Gromacs web site. I want to generate different trajectories on my system, and I used an .mdp file in which I set gen_seed = -1 together with gen_vel = yes and continuation = no to do this quickly. If I

Re: [gmx-users] initial velocities analysis

Anna Marabotti wrote: Dear gmx-users, sorry for my trivial questions, but I didn't find an answer searching in the Gromacs web site. I want to generate different trajectories on my system, and I used an .mdp file in which I set gen_seed = -1 together with gen_vel = yes and continuation =

[gmx-users] making index file

Hello, I am trying to make two different groups from residues below. one under the name Solute (residues a and b) and the other for solvent (residue c, SOL). The only way I know now is to do this by splitting the list of atom numbers [system] (default index file), from 1 to 362 and creating a new

Re: [gmx-users] making index file

jojo J wrote: Hello, I am trying to make two different groups from residues below. one under the name Solute (residues a and b) and the other for solvent (residue c, SOL). The only way I know now is to do this by splitting the list of atom numbers [system] (default index file), from 1 to

RE: [gmx-users] dihedral function type 9 in rtp file

http://lists.gromacs.org/pipermail/gmx-users/2010-August/053255.html Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu -

RE: [gmx-users] dihedral function type 9 in rtp file

Thanks Dallas. Forgot to search the mailing list this time. Jianhui Date: Thu, 26 Aug 2010 08:39:17 +1000 From: Dallas Warren dallas.war...@monash.edu Subject: RE: [gmx-users] dihedral function type 9 in rtp file To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID:

[gmx-users] Inconsistent charges in OPLS-AA residues ASPH and GLUH

Hi, while having a closer look at the topologies of aspartic- and glutamic-acid in OPLS-AA, I noticed that the charges of the carboxylic oxygen atoms are not consistent in the protonated forms of those residues: from ffoplsaa.rtp of gromacs 4.0.7: [ ASPH ] [ atoms ] Nopls_238 -0.500

Re: [gmx-users] How to tell if the molecule is correctly reduced?

- Original Message - From: Roland Schulz rol...@utk.edu Date: Thursday, August 26, 2010 3:06 Subject: Re: [gmx-users] How to tell if the molecule is correctly reduced? To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, if the gro file written by pdb2gmx contains the same

[gmx-users] Fatal error:There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.62125 nm

Hi,   I am doing a minimization in GMX 4.5-beta3. The system includes 256 DPPC and  9899 SOL. I used a command:  mdrun -v -deffnm min Then an error occured, Program mdrun_mpi, VERSION 4.5-beta3 Source code file: domdec.c, line: 6428 Fatal error: There is no domain decomposition for 8 nodes that

Re: [gmx-users] Fatal error:There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.62125 nm

Hi, 4.5beta compiled without MPI uses by defaults all cores using threads. You can run it with mdrun -nt 1 to run only on one core and thus avoid parallelization errors. Why the minimum cell size is 6.6nm (which is huge) I'm not sure. It should write in the log file why mdrun computed the minimum

Re: [gmx-users] Fatal error:There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.62125 nm

- Original Message - From: Roland Schulz rol...@utk.edu Date: Thursday, August 26, 2010 13:04 Subject: Re: [gmx-users] Fatal error:There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.62125 nm To: Discussion list for

[gmx-users] How to calculate the distances

Hi all, I guess the question I'm going to ask probably is a bit simple to those who know, well. After MD, I got a dimer, how could I get the distance of those two proteins, the centre of mass distance. In this simulation, there were six involved, but I only want to calculate the two of them.

Re: [gmx-users] How to calculate the distances

- Original Message - From: #ZHAO LINA# zhao0...@e.ntu.edu.sg Date: Thursday, August 26, 2010 15:17 Subject: [gmx-users] How to calculate the distances To: gmx-users@gromacs.org gmx-users@gromacs.org P {margin-top:0;margin-bottom:0;}