[gmx-users] To calculate surface area of of simulated protein

Hello gmx users.. Can anybody tell me is there any possibility to calculate the surface area of the protein before and after the simulation. waiting for u'r reply.. -- Bharath.K.Chakravarthi Ph:9535629260 -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] To calculate surface area of of simulated protein

On 23/04/2010 5:06 PM, Bharath.K. Chakravarthi wrote: Hello gmx users.. Can anybody tell me is there any possibility to calculate the surface area of the protein before and after the simulation. Rather than ask the list, start with looking at the programs by topic list in the manual, section

Re: [gmx-users] make_edi

Hi Vijaya, what version of Gromacs is this and how big do the trr files have to be so that the segv shows up? Carsten On Apr 22, 2010, at 6:56 PM, vijaya subramanian wrote: Hi When I run make_edi with a small eigenvec.trr file it works, but gives me a segmentation fault when I input

[gmx-users] Re: Re: The problems of controling one atom through modifygromacs

Hi Carsten, Thank you very much. I add some code like if（(cr-dd-ga2la[my_atom-1].cell==0)(n==cr-dd-ga2la[my_atom-1].a)).Then it perform very well. chuan Date: Thu, 22 Apr 2010 09:54:22

[gmx-users] Freezing a portion of a protein during simulation

Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file containing the desired

Re: [gmx-users] Freezing a portion of a protein during simulation

Anirban Ghosh wrote: Hi ALL, I want to do a MD simulation by restraining (freezing) the helical portions and allowing only the loop regions to move. I tried doing this by applying heavy restrain on the helical residues by generating a .itp file with the genrestr command with an index file

RE: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Hi, I ran it just for a few steps. Please give numbers, not much and slowly increasing don't tell me much. Berk Date: Thu, 22 Apr 2010 06:47:42 -0400 Subject: Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations From: jampa...@gmail.com To: gmx-users@gromacs.org Dear

[gmx-users] g_wham giving flat free energy

Hi everyone.  I'm having some trouble using g_wham to analyze some results.  I have some simulations from gromacs 3.3 using the pull code.  I'm using the latest version of g_wham to analyze the results, which the help file says is ok, using the -ip option.   I've gotten almost everything to

RE: [gmx-users] make_edi

Hi CarstenI checked again and the segmentation fault appears to be unrelated to file size. I obtained theeigenvector.trr files that give a seg fault using the g_covar -nofit option as I had already fit the datausing trjconv -fit rot+trans. This would mean the reference structure file is not

Re: [gmx-users] .mtx file

Hello Justin, I am using Gromacs 4.0.5 version. I am getting the same error without specifying -o option. Nilesh On Thu, April 22, 2010 5:07 pm, Justin A. Lemkul wrote: Nilesh Dhumal wrote: Hello Justin In manual (Manual-4.0) and g_nmens -h (help), the extension of output file is

Re: [gmx-users] .mtx file

Nilesh Dhumal wrote: Hello Justin, I am using Gromacs 4.0.5 version. I am getting the same error without specifying -o option. You could try upgrading to 4.0.7, but I don't know if there have been any changes in the code that would affect this behavior. Otherwise, submit a bugzilla.

[gmx-users] grompp error(Segmentation fault)

I'll be most thankful if any one would be able to help me with the following problem. While running the grompp (in both single and double precision) command I get a Segmentation fault (core dumped) error. The error persist even after recompiling the GROMACS with gcc-4.4.3(previously I was

Re: [gmx-users] grompp error(Segmentation fault)

On 24/04/2010 7:28 AM, Arik Cohen wrote: I'll be most thankful if any one would be able to help me with the following problem. Giving more complete information will give you a much better chance. It's not our job to be the family doctor and ask questions :-) What GROMACS version is it? Does

[gmx-users] Hydrocarbon system, help on mdp setting +output file

Dear gmx users, I am trying to run grompp program to preprocess the input files. input gro file contains coordinates of a stack of hexane molecules (256 molecules).. 1- In the outpout file I see two notes. As with note 1, Could you please help me understand what wrong with charge group is.

Re: [gmx-users] Hydrocarbon system, help on mdp setting +output file

Moeed wrote: Dear gmx users, I am trying to run grompp program to preprocess the input files. input gro file contains coordinates of a stack of hexane molecules (256 molecules).. 1- In the outpout file I see two notes. As with note 1, Could you please help me understand what wrong

[gmx-users] simulated annealing (SA)

Hi all I have some questions about simulated annealing (SA): 1) Is SA a optimization method? or a minimization method? 2) Steps in md simulation are as follow: (a) minimization (b) equilibration (c) production run (d) analysis so, where do SA lie in previous line? (before or after

[gmx-users] simulated annealing (SA)

Hi all For simulated annealing simulation, except things mentioned as follow,what things should be in mdp file? integrator dt nsteps annealing annealing npoints annealing time annealing temp tcoupl tc_ grps tau_t ref_ t Any help will highly appreciated! -- gmx-users mailing list

[gmx-users] Cutoff value during lipid shrinking using inflategro.pl script

Hello all, I am trying to do shrinking of lipids using inflategro.pl script. So anyone can suggest me *how much cut off value* should I give to remove overlapped lipid residues. I have to give *cutoff from starting step or at final step*of shrinking. perlinflategro.plconfout.gro0.95

[gmx-users] large oscillation in mean force with constraint

Hi, I am trying to calculate the PMF of two peptides using constraint in gromacs 4.0.5. But, I am finding a very large oscillation( from -1000 to +1000) in the force that is being printed in pullf.xvg file . Is this oscillation normal ? In that case at any distance, the mean force will be