Re: [gmx-users] list of published papers

http://www.gromacs.org/Documentation/Gromacs_papers - Original Message - From: milad ekramnia Date: Saturday, May 22, 2010 14:14 Subject: [gmx-users] list of published papers To: gmx-users@gromacs.org > Dear Gromacs users > I can remember up to one year ago oldwww.gromacs indexed a list

[gmx-users] list of published papers

Dear Gromacs users I can remember up to one year ago oldwww.gromacs indexed a list of published papers which were based on gromacs platform . but now I can't find it anymore . Anyone knows whether the list is still on the server or it has been removed ? regards -- Milad Ekramnia Physics Depart

Re: [gmx-users] specifying interaction energy between residues

- Original Message - From: Gene Polovy Date: Saturday, May 22, 2010 11:00 Subject: Re: [gmx-users] specifying interaction energy between residues To: Discussion list for GROMACS users > I'm trying to simulate three alpha spectrin repeats (R15, R16, > R17) using a structure based C-alpha

Re: [gmx-users] specifying interaction energy between residues

I'm trying to simulate three alpha spectrin repeats (R15, R16, R17) using a structure based C-alpha model: http://smog.ucsd.edu/. My task is first to modify the sample .mdp file available at http://smog.ucsd.edu/GromacsTutorial.html. I'm having some difficulty figuring out what to set rlist, rc

Re: [gmx-users] specifying interaction energy between residues

- Original Message - From: Gene Polovy Date: Saturday, May 22, 2010 8:37 Subject: [gmx-users] specifying interaction energy between residues To: gmx-users@gromacs.org > Hi There, > > I'm trying to run a course grained (c alpha) simulation of a Letting us know more about what kind of co

Re: [gmx-users] Re: OPLS-AA/L force field

you zou wrote: Hi again, Sorry, I have one question now, what is the meaning of structure? I think coordinates is structure, is it true? Yes, a coordinate file contains a structure. If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms are different from top file and

Re: [gmx-users] Break down of total energy

- Original Message - From: Moeed Date: Saturday, May 22, 2010 4:51 Subject: [gmx-users] Break down of total energy To: gmx-users@gromacs.org > Hello Justin, > > As for exclusions, in the manual I see 1-4 interactions refer to carbon atoms > on the backbone. I do not know if it makes sen

[gmx-users] Re: OPLS-AA/L force field

Hi again,Sorry, I have one question now, what is the meaning of structure? I think coordinates is structure, is it true?If it is true, when I used "editconf -f drg.pdb -o drg.gro" number of atoms are different from top file and editconf can not add hydrogens to drg.gro. If Gromacs can handle .p

[gmx-users] specifying interaction energy between residues

Hi There, I'm trying to run a course grained (c alpha) simulation of a protein and I'd like to know how/where I can define heterogeneous native interaction energies between residues. Is it under [ pairs ] in the topology file? In other words, I'd like to use a flavored model rather than a vanil

Re: [gmx-users] g_clustsize output

Hello, Thanks for the response. g_clustsize outputs two xpm files of the weighted and non-weighted cluster size vs time. Is there another way for me to get number of clusters vs cluster size? Thanks, Mike On May 20 2010, David van der Spoel wrote: On 2010-05-20 04.55, toma0...@umn.edu

[gmx-users] g_analyze negative

Hello gmx-users, I am attempting to use g_analyze to find the error estimate on the average volume of my system. Using an .xvg file with my volume data and the -ee flag I receive the following message. Found only 1 number on line, assuming no time is present. Read 1 sets of 611700 points, dt

[gmx-users] g_densmap

Dear Friends When I applied the g_densmap to my system, my molecule appear in the corner of the xpm file and white diffuse regions (maybe by the box rotations) appear.I used this sequence to obtain the gro file (gro reference used for rotate the box to coincide with the XY molecular plane. The

[gmx-users] Break down of total energy

Hello Justin, As for exclusions, in the manual I see 1-4 interactions refer to carbon atoms on the backbone. I do not know if it makes sense if I enter a number more than 5 (hexane has only 6 carbons), However, I did so and I changed nrexcl from default value of 3 to 19 ( to exlude all interaction

[gmx-users] reproducibility of PMF plot with two different starting structures

Your run is not converged. You could (i) run more slowly, (ii) run lots of these non-equilibrium runs and treat them appropriately, or (iii) use an equilibrium method. In any event, I suggest that you begin by (iv) repeat the run for both poses with different random seeds to see how much of

Re: [gmx-users] stepsize too small ... but potential energy negative!

Moreover, the problem is not the potential energy, but the force that must converge. The "inf" there about force and about atom 1 tells me that the computed force has problems, indeed. Which is atom 1 ? Is the protein Nter neutral or charged ? Or is atom 1 an atom from the ligand ? Cheers L

Re: [gmx-users] stepsize too small ... but potential energy negative!

Dear Anna, are you talking about a system "in vacuo" or in solvent ? If you have placed the protein in water w/o minimizing it before solvation, probabily an "in vacuo" minimization could be useful for your system before moving into the solvated case. Moreover, are you sure that the protein doe

[gmx-users] stepsize too small ... but potential energy negative!

Dear gmx-users, I tried to minimize my systems formed by a protein obtained by homology modelling procedure, in one case with a ligand inside, in the other case in the apo form. All worked fine until the minimization step: when I launched mdrun, the well known "stepsize too small..." communication

Re: [gmx-users] PCA

Hi Pawan, You may want to read up on PCA in some elementary multivariate statistics textbook to get a better grasp on what it does and how it's done. > I have a little concept problem regarding principal component analysis. So > my question is about ED sampling are as follows: > > 1. I have read