Re: [gmx-users] negative diffusion constant by g_msd -mol option

[EMAIL PROTECTED] wrote: Hello all, I calculate diffusion constant for each individual molecule using g_msd and -mol option. There are some negative values in the output file. Diffusion constant is always positive value, isn't it? I don't know how negative value is calculated. I am using gromac

Re: [gmx-users] compressibility value for SPC water

chetana baliga wrote: Dear all, I read from the mailing list archives, that it is not just the value of tau_p but the ratio of compressibility to tau_p which matters in Berendsen presure coupling. I am using SPC water as the solvent. Is there any ideal value for compressibility to be used fo

Re: [gmx-users] 2 questions: pdb2gmx and genbox

Hi William, It may be a good idea to follow the tutorial at: http://nmr.chem.uu.nl/~tsjerk/MDCourse/ It doesn't take too much time and will give you a fair idea of using the program, with the options, the file types, etc. If you look at the top of the output from pdb2gmx you will see the flag

回复： Re: [gmx-users] PMF calculation

Dear Mr Mark Abraham: Can you tell us the details of performing PMF procedures? Thank you very much! Best wish for you! Mark Abraham <[EMAIL PROTECTED]> 写道： > Dear all, > I am working on a tripeptide and would like to calculate Potential > Mean Force for the tripeptide. Suggestions to cal

Re: 回复： Re: [gmx-users] PMF calculatio n

xi zhao wrote: > Dear Mr Mark Abraham: > Can you tell us the details of performing PMF procedures? Thank you > very much! > Best wish for you! plz start by reading the manual. if you have *specific* questions you can put them on the mailing list. > > */Mark Abraham <[EMAIL PROTECTED]>/* 写道：

[gmx-users] RAM MEMORY USAGE FOR g_cluster/g_rms

Dear GMX users, I am facing Memory problem while running g_cluster and g_rms (for RMSD matrix) calculations. The output of g_rms command is as follows. # Building RMSD matrix, 50001x50001 elements element 9040; time 9040.00 Fa

Re: [gmx-users] RAM MEMORY USAGE FOR g_cluster/g_rms

[EMAIL PROTECTED] wrote: Dear GMX users, I am facing Memory problem while running g_cluster and g_rms (for RMSD matrix) calculations. The output of g_rms command is as follows. # Building RMSD matrix, 50001x50001 elements elem

[gmx-users] disallowed residue calculation

Dear gmx users, Is there any gmx command to plot the number of residues in disallowed region of the Ramachandran plot. g_rama and xrama doesnot have such options to calculate the same. -Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Bi

[gmx-users] Essential Dynamics Sampling (EDS) MD

Dear all, I'm resending this message (please see below) with some additional info, hoping that someone can at least point me to what I should check. I ran the simulation with the -debug flag and got some "nan" values in mdrun.log: dekin = nan, ekin = 175815 vcm = ( nan nan nan) m

[gmx-users] error while compilation of Gromacs 3.3.1.....

Dear Gromacs users, I am installing the Gromacs version 3.3.1 on the SGI Octane with IRIX 6.5 R12000 system. I could successfully installed fftw package and trying the compile gromacs. I am getting the following at the end of the 'make' command : These are the last few lines after the mak

Re: [gmx-users] RAM MEMORY USAGE FOR g_cluster/g_rms

Yes, the Machine is a 64bit, sparc, solaris. Any setting could be done for using the required memory? ## Message: 3 Date: Thu, 11 Jan 2007 10:57:56 +0100 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] RAM MEMOR

Re: [gmx-users] RAM MEMORY USAGE FOR g_cluster/g_rms

[EMAIL PROTECTED] wrote: Yes, the Machine is a 64bit, sparc, solaris. Any setting could be done for using the required memory? check what size the pointers are, maybe you have to use another type for the array in order to be able to have more than 2Gb arrays, but you will have to read documen

Re: [gmx-users] error while compilation of Gromacs 3.3.1.....

Am Donnerstag, 11. Januar 2007 11:52 schrieb sharada: > R12000 system. I could successfully installed fftw package and trying the > compile gromacs. I am getting the following at the end of the 'make' > command : which compiler are you using? Martin ___

Re: Re: [gmx-users] error while compilation of Gromacs 3.3.1.....

I am using the MIPSpro Compilers Version 7.3 . Is there a problem with that version ? I had installed the Gromacs version 3.01 and version 3.2 using the same compilers earlier there was no problem why now.? Thanks for the reply regards sharada -- Original Message

Re: [gmx-users] Essential Dynamics Sampling (EDS) MD

Dear Ran, this could mean that you have problems fitting to your reference structure. Lars Ran Friedman wrote: Dear all, I'm resending this message (please see below) with some additional info, hoping that someone can at least point me to what I should check. I ran the simulation with the -d

[gmx-users] the box margin plot in VMD

You can use Gaussian98 cube format: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html Make a file like this: title1 title2 0 x-origin y-origin z-origin 1 x-width 0.0 0.0 1 0.0 y-width 0.0 1 0.0 0.0 z-width 1 0 0 0 0 0 For example, if you want a cube that has a corner at (0,0,

Re: [gmx-users] Essential Dynamics Sampling (EDS) MD

Dear Lars, GMX users: It doesn't seem to be the problem, as the initial RMSD from reference structure =0.16037 nm I also get: Large VCM(group rest): nan, nan, nan, ekin-cm: nan In the log file. Ran. Lars Schaefer wrote: > Dear Ran, > this could mean that

[gmx-users] Has the forces for virtual sites in the trr file been reditributed?

Dear GROMACS list members, I have another question on the force data in trr files. For the TIP4P model, there is one virtual site. I am wondering if the forces on the virtual sites and the other related atoms have been redistributed before they are written in the trr file. Thank you ve

[gmx-users] center of mass motion in lipid bilayer

Hello, everyone: I have a system which is composed of a lipid bilayer and water layers upon each monolayers. Now the problem is that after the simulation, the lipid bilayer shift upward inside the simulation box , and makes the upper water layer thinner, while the lower water layer thicker. In md

Re: [gmx-users] Has the forces for virtual sites in the trr file been reditributed?

Pu Liu wrote: Dear GROMACS list members, I have another question on the force data in trr files. For the TIP4P model, there is one virtual site. I am wondering if the forces on the virtual sites and the other related atoms have been redistributed before they are written in the trr file.

Re: [gmx-users] center of mass motion in lipid bilayer

Jian Dai wrote: Hello, everyone: I have a system which is composed of a lipid bilayer and water layers upon each monolayers. Now the problem is that after the simulation, the lipid bilayer shift upward inside the simulation box , and makes the upper water layer thinner, while the lower water

[gmx-users] box size for simulation of membrane protein

I am going to start by quoting: Chapter 3 of the Gromacs manual (page 14) "length of each box vector must exceed the length of the macromolecule in the direction of that edge plus two times the cutoff radius Rc"Then it states: "It is common to compormize in this respect and make the solvant

Re: [gmx-users] error while compilation of Gromacs 3.3.1.....

Am Donnerstag, 11. Januar 2007 13:39 schrieb sharada: > I am using the MIPSpro Compilers Version 7.3 . Is there a problem with that > version ? I had installed the Gromacs version 3.01 and version 3.2 using > the same compilers earlier there was no problem why now.? Thanks for > the reply I wa

[gmx-users] hbhelix,hbond,hbnum files

Hi, I have the following problem: My system consists of a capped three-alanine residues embedded in a box with 750 water molecules. I want to analyze the hydrogen bonds formed in each frame. In this respect, I used the -hx option to investigate the exact contributors of the hbonds in each fra

[gmx-users] micelle center of mass rdf to water

I have a micelle in a box of water. I want to get the radial distance profile of different atom types from the center of mass of the micelle. This is not as simple as might be imagined because centering the micelle does not keep the micelle together, but splits it to the corners of the unit cel