Re: [gmx-users] "Lam" is not required for running parallel job

- Original Message - From: [EMAIL PROTECTED] Date: Wednesday, February 13, 2008 5:40 pm Subject: [gmx-users] "Lam" is not required for running parallel job To: gmx-users@gromacs.org > Dear Users, > > Lam doesn't seem to be essential for running parallel job. An MPI library is essential

Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist option

On Wed, 13 Feb 2008 00:46:33 +0200 "OZGE ENGIN" <[EMAIL PROTECTED]> wrote: Xavier, The output file of g_cluster with -dist option then gives the histogram of rmsd value distribution, is it? yes If it is the case, after plotting these data,I observe that the distribution resembles a gaussia

[gmx-users] "Lam" is not required for running parallel job

Dear Users, Lam doesn't seem to be essential for running parallel job. Because in one of our Xeon machine with quardcore 1.6 Ghz processor and with 6 nodes we installed parallel version of gromacs (version 3.3.1) and its running without any problem. Lam is not installed in this machine still it i

Re: [gmx-users] adding atoms in PDB file

- Original Message - From: s lal badshah <[EMAIL PROTECTED]> Date: Wednesday, February 13, 2008 4:35 pm Subject: [gmx-users] adding atoms in PDB file To: gmx-users@gromacs.org > Hi all, > I am new to gromacs andI want to add atoms to pdb file , what is > the method for this? You use a

[gmx-users] adding atoms in PDB file

Hi all, I am new to gromacs andI want to add atoms to pdb file , what is the method for this? Regrads, SYED LAL BADSHAH M.Phil Scholar NCE in Physical Chemistry, University of Peshawar. NWFP,Pakistan. Cell # 03349060632. Send instant messages to your online friends http://uk.messenger.yaho

Re: [gmx-users] RAM memory

I’m working with membrane-peptide simulations of ~30,000 atoms. The box features are 2 quad-core processors 2.00 GHz, 2x6MB Cache L2 and 1333 MHz FSB. As I said, I read an E. Lindahl’s presentation from Gromacs Workshop 2007 Talks. That says “Gromacs normally uses 256MB to 1GB per process, dependin

Re: [gmx-users] Generate topology file for Gromacs a from Accelrys or pdb file

Tandia, Adama wrote: Dear ALL, I have generated from Accelrys (Materials Studio) a structure composed of a substrate topped by a layer of organic molecules. The structure can be saved into a .pdb format. Is there out there a tool that I could use to generate the corresponding topology file for

Re: Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist option

Xavier, The output file of g_cluster with -dist option then gives the histogram of rmsd value distribution, is it? If it is the case, after plotting these data,I observe that the distribution resembles a gaussian type, its mean is located around 0.4 nm. This value is bigger compared to yours. I

Re: [gmx-users] RAM memory

zazeri wrote: Are 4GB of RAM memory enough to run the gromacs with the maximum performance in a computer with dual quad-core processors? If the performance is smaller, is the decreasing significant? I´ve read in somewhere Erik Lindahl suggesting 8GB... It depends how big your simulation syste

Re: [gmx-users] the 2 nd column of the output of g_cluster with -dist option

On Tue, 12 Feb 2008 23:55:35 +0200 "OZGE ENGIN" <[EMAIL PROTECTED]> wrote: Hi all, What does the second column of the output file of g_cluster with -dist option stand for? Its title is a.u. I think it is atomic unit? In the manual, it is not described. I believe a.u. stands for arbitrary un

[gmx-users] the 2 nd column of the output of g_cluster with -dist option

Hi all, What does the second column of the output file of g_cluster with -dist option stand for? Its title is a.u. I think it is atomic unit? In the manual, it is not described. Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___

Re: [gmx-users] RSS feed for gromacs.org?

Moore, Jonathan (J) wrote: Is there an RSS feed for the "latest news" from gromacs.org? I discovered this link: http://www.gromacs.org/index2.php?option=com_rss&no_html=1 But it says you aren't authorized to view without logging in

Re: [gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix

On Tue, 12 Feb 2008 20:56:04 +0200 "OZGE ENGIN" <[EMAIL PROTECTED]> wrote: Hi all, I have three questions. 1)In order to get the rmsd distribution of all the conformations, I used g_rmsd. In the help menu, it is stated that g_rmsd compares the structure given by -s and compares it to the ot

[gmx-users] RAM memory

Are 4GB of RAM memory enough to run the gromacs with the maximum performance in a computer with dual quad-core processors? If the performance is smaller, is the decreasing significant? I´ve read in somewhere Erik Lindahl suggesting 8GB... Thanx in advance! Zaz. Abra sua conta no Yahoo!

[gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix

Hi all, I have three questions. 1)In order to get the rmsd distribution of all the conformations, I used g_rmsd. In the help menu, it is stated that g_rmsd compares the structure given by -s and compares it to the others which are given by -f option. Consequently, I can not get the rmsd betwee

[gmx-users] Temperature of the system when using stochastic dynamics in vacuum

Hi all, Recently, I run a carbon nanotube in vacuum using stochastic dynamics (Gromacs 3.3.1, integrator=sd) at 300K (ref_t=300.0) for 800 ps. The number of atoms of the CNT is about 5000, and the tube is left free to vibrate except for a few atoms are position restrained. When I set the tau_t=100

[gmx-users] Generate topology file for Gromacs a from Accelrys or pdb file

Dear ALL, I have generated from Accelrys (Materials Studio) a structure composed of a substrate topped by a layer of organic molecules. The structure can be saved into a .pdb format. Is there out there a tool that I could use to generate the corresponding topology file for Gromacs? Thank you in

[gmx-users] RSS feed for gromacs.org?

Is there an RSS feed for the "latest news" from gromacs.org? I discovered this link: http://www.gromacs.org/index2.php?option=com_rss&no_html=1 But it says you aren't authorized to view without logging in Jonathan Jonathan Moore, Ph.D. Research and Engineering Scien

Re: [gmx-users] adding a polar Hydrogen atom to pdb file

Quoting [EMAIL PROTECTED]: > Hi all, > i have to edit a pdb file that will have all polar hydrogens & non polar > hydrogens.while dealing with pdb2gmx commands it only adds polar hydrogens > not non polar hydrogens.So how to get the pdb files having polar as well > as non polar atoms in a pdb file

[gmx-users] adding a polar Hydrogen atom to pdb file

Hi all, i have to edit a pdb file that will have all polar hydrogens & non polar hydrogens.while dealing with pdb2gmx commands it only adds polar hydrogens not non polar hydrogens.So how to get the pdb files having polar as well as non polar atoms in a pdb files. i will be thankful for any positi

Re: [gmx-users] Re: Wheter the drift velocity has been removed from calculating the temperature?

Hu Zhongqiao wrote: > I wonder if the drift velocity has been removed from calculating the > temperature for a non-equilibrium MD in which a directional movement for > a group exists due to external force applied. Yes it is. Please check the source code in src/mdlib/update.c

[gmx-users] Re: Wheter the drift velocity has been removed from calculating the temperature?

>> I wonder if the drift velocity has been removed from calculating the >> temperature for a non-equilibrium MD in which a directional movement for >> a group exists due to external force applied. > Yes it is. Please check the source code in src/mdlib/update.c Thanks, David. Then h

Re: [gmx-users] Hello

Hi Anamika, It would be good to do some background reading on MD. For this issue, you most likely should read: http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions Cheers, Tsjerk On Feb 12, 2008 11:14 AM, Anamika Awasthi <[EMAIL PROTECTED]> wrote: > Dear Gromacs users, > I am b

Re: [gmx-users] Hello

Quoting Anamika Awasthi <[EMAIL PROTECTED]>: > Dear Gromacs users, > I am beginner in using using GROMACS and MD simulations, Please help > me in solving my problem. > I simulate my protein for 5 ns and after simulations RMSD in C-alpha is > showing a big fluctuation after 3 ns and til

[gmx-users] Hello

Dear Gromacs users, I am beginner in using using GROMACS and MD simulations, Please help me in solving my problem. I simulate my protein for 5 ns and after simulations RMSD in C-alpha is showing a big fluctuation after 3 ns and til 3.5 ns to 4.5 ns its fine and again its showing fluctua