Re: [gmx-users] problem in binding free energy calculation and setting Lambda

Dear Meisam, Take a look at Justin Lemkul's tutorial. It's very well explained step by step: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html Good luck, Marcelo On Tue, Sep 27, 2011 at 10:49 AM, meisam valizadeh kiamahalleh < meisam...@gmail.com> wrote:

[gmx-users] Number of water molecules

Dear All. Is there any tool (or set of tools) in GROMACS which allows me to calculate #H2O vs time inside a pocket or in between two fragment of a protein? Any help and/or hint will be fully appreciated. Marcelo -- MSc. Marcelo F. Masman Department of Molecular Neurobiology, Faculty of Mathematic

Re: [gmx-users] Concatenate .edr file

Use eneconv program Marcelo On 10/20/07, Qi Yan <[EMAIL PROTECTED]> wrote: > > Does anybody really know how to concatenate .edr file, since "trjcat" > concatenates only trajectory files. > > ___ > gmx-users mailing listgmx-users@gromacs.org > http:

[gmx-users] H-bond problems

Dear All, I am running a protein-drug simulation. I have got a 10 ns simulation and I want to know the number of protein/drug H-bonds, but I get this error message: Found 4 different hydrogen bonds in trajectory Merging hbonds with Acceptor and Donor swapped Segmentation fault This error messag

[gmx-users] Freezing part of the molecules!!!

Hi all!!!   I am trying to run a MD simulation with part of my system frozen. I was looking into the manual but I couldn't find the answer since the manual says the way for freezing complete groups. I would like to freeze only a part of my protein and permit the completed optimization of the rest.

Re: [gmx-users] Getting out of the box!!!

e to linear with the protein as comm_group. Now please read the manual on periodic boundary conditions and for further reference search the mail list ( e.g. "periodic boundary conditions", "PBC", "jumping", etc...)Tsjerk On 5/10/06, Marcelo Fabricio Masman < [EMA

[gmx-users] Getting out of the box!!!

Hello gmx users:   I am running a very common MD simulation and the protein system is getting OUT of the box after approximately 200 ps. I have tried several things. Does it happen very frequently? (common mistake) Is there any way to keep, during the whole calculation, the protein system into the

[gmx-users] Fatal error!!!!

Hello all,   I am trying to run my MD and I have this fatal error:   Grid: 0 x 0 x 0 cellsFatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]  I really do not how to fix it. Maybe I have a error in my dm.mdp file. Here it is:   **

Re: [gmx-users] pdb2gmx atom not found

Hello Una, I am not a expert... but I think you have to use NZ (without 1) for LYSH. I had a similar problem. I hope it is useful for you.   bye   Marcelo    On 3/9/06, Una Bjarnadottir <[EMAIL PROTECTED]> wrote: Dear users,I keep getting this error when starting runs;Opening library file aminoacid

[gmx-users] Hi all!

Hi all!!! I am using the programme grompp (double precision) and the programme genion to make  "neutral" .top and .tpr files. But after change the quantity of H2O molecules and add the line with the necessary Na+ ions I am still having WARNING and the charge is STILL  negative. What happend? What a

[gmx-users] Fatal error!!!!!!!!!!!!!!!!!!!!!

Hello, I am Marcelo and I am a new user of Gromacs. When I use the programme pdb2gmx the following  fatal error happens:   Fatal error: Chain identifier 'S' was used in two non-sequential blocks (residue 7, atom 101)   The thing is that I am not using "chain indentifiers. Could someone help me, ple