[gmx-users] Gramicidin A

Hello everyone,I am interested in simulating gramicidin A channel in DPPC membrane.I noticed there were few papers already published on this particularlyBiophysics Journal Vol. 82 June 2002, by de Groot, Tieleman, Pohl and Grubmuller. Does anyone has the structure along with the topology files so t

Re: [gmx-users] grompp is lying...

Hi Ken, check if the cpp is installed and correctly set in your .mdp file. That was the most common reason for me to get this kind of error. ...Oliver Ken Rotondi wrote: --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line:

[gmx-users] pdb2gmx residue error

Hi, I am trying to do a simple NaCl solvation and MD run using GROMACS. I have 4 atoms in my (.xyz) file for the 2 Na's and 2 Cl's. I convert the (.xyz) to (.pdb) using babel. Afterwards, I try to generate the topology file using pdb2gmx program and it generates an error. I am using the 43a1 f

Re: [gmx-users] grompp is lying...

You may use -pp for grompp to see what the processed top looks like. It could be true that some where, C-like directive is not correct or sections are incomplete.Regards,Yang Ye- Original Message From: Ken Rotondi <[EMAIL PROTECTED]>To: Discussion list for GROMACS users Sent: Saturday, July

[gmx-users] grompp is lying...

I know, enigmatic subject, but it's true. The program is GROMACS 3.3.1 running on a Fedora linux box. I'm trying to do the most simple thing, charge balance a system with 1 protein and solvent. When I try to run grompp to generate a run input file for genion there is a fatal error stating that

[gmx-users] Sodium Channel

Hi everyone,Did anyone do MD simulations on voltage gated sodium channel?I could find papers on MD simulations on KcsA potassium channels and stuff, but I could not find anywhere MD simulations on sodium channels. Thanks in advance,-Vishy-- Viswanadham Sridhara,Graduate Research Assistant,Old Domin

[gmx-users] Script for Gromacs - RunGMX 3.2

Hi all. Well, I've been working in this for some time now, and it now seems to be a stable and clean and also "good looking" version. Since I think I'm not the only one that, instead of making one long simulation, prefers to make some or many simulations one after the other, this might be of use.

[gmx-users] How to fix the position of Au in my MD.

I am a new user of Gromacs and am conducting a MD simulation of SAM(self-assembled-monolayer) in gold(111) surface. Here is my .itp .top and .mdp file during energy minimization. I want to fix the position of gold atoms, but in simulation the gold atoms run around. Who can help me? Thank

[gmx-users] R.M.S.I.P. between two halves of same simulation

Hi Tsjerk, I computed r.m.s.i.p. between eigvectors trajectory for two halves of the same simulation, I expected it should be higher value than its other eigenvectors. But in my case it is showing less than the others, For example, please look at the below r.m.s.i.p matrix Wild

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Hi Tsjerk, Oops, I am sorry and thanks for your help and providing me the program. With thanks! B.Nataraj On Fri, 28 Jul 2006 13:35:48 +0200, "Tsjerk Wassenaar" <[EMAIL PROTECTED]> said: > Hi Raja, > > Okay, you're not using the eigenvectors, you're using the > eigenvalues... The eigenvectors a

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Hi Raja, Okay, you're not using the eigenvectors, you're using the eigenvalues... The eigenvectors are written to a .trr or .xpm file, as NxN matrices. You can try the attached script (which I got from Isabella Daidone) on the .xpm file. Good luck, Tsjerk On 7/28/06, raja <[EMAIL PROTECTED]>

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Hi Tsjerk, Here is the script I am using. I already checked the value computed by this script with manually computed value for small set of 3 eigen vectors in each file. As you already know the formula, so please check it up by yourself. More I am not a regular programmer so this script is written

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Hi Raja, I really don't get it. From the definition it follows directly that if you have the same sets of eigenvectors, the RMSIP will be 1. Each eigenvector from a set gives an inproduct of 1 with itself and of 0 with any of the others, yielding a total of 10 for the double sum... etc. If you us

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Hi Tsjerk, Thanks for your reply. I used identical values of 10 eignevectors in two different file to compute r.m.s.i.p. I have pasted the link of the article from where I used the formula for r.m.s.i.p. More for some other cases of non-identical values, it slightly exceeds the value of 1 (e.g., 1.

Re: [gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Hi Raja, Did you use the same eigenvectors from the same simulation over the same stretch of time? For two (parts of a) simulation(s) of the same system, the RMSIP value will only converge to one in the limit of infinite time, or on long time scales at least. The eigenvectors obtained from two di

[gmx-users] R.M.S.I.P for identical eigenvectors not equal to 1 ?

Dear all, I have written small perl script to compute R.M.S.I.P.(Root mean square internal product) for comparing two eigen vectors set from two different simulation. I compared first 10 eigen vectors of each set. The strange thing is that while I compare eigen vectors of same simulation, it is sh