Re: [gmx-users] changing protonation state of a residue during a simulation

On 5/15/13 7:14 PM, Payman Pirzadeh wrote: Hello, I am simulating a protein using side chain pKa values estimated from PROPKA based on crystal structure of the protein. I re-estimated the pKa of side chains after running 10 independent replica of 50ns (500ns in total) of NPT simulations. It tur

Re: [gmx-users] g_dist problem in Implicit solvent

On 5/15/13 7:15 PM, Tong Li wrote: Hi Justin, I really appreciate your reply! I finally solved the problem: change the machine… I have no idea why this happens, the machine I run simulation on is HP Z600, Ubuntu. The package is directly installed from the ‘Ubuntu software center’. This syste

Re: [Spam:*****] [gmx-users] REMD analysis

The plots that I showed in my last mail were for all replicas. I tried plotting the first 500 ps of replica_index and replica_time files. I think the plots look fine, and there could be problem with the plotting tool . Here the link for both files , https://www.dropbox.com/s/2g16mlxfsme4rx2/replica

Re: [gmx-users] changing protonation state of a residue during a simulation

Hello, I am simulating a protein using side chain pKa values estimated from PROPKA based on crystal structure of the protein. I re-estimated the pKa of side chains after running 10 independent replica of 50ns (500ns in total) of NPT simulations. It turned out that the average pKa of a surface Glu w

Re: [gmx-users] xtc2dcd conversion

Hi, you can use catdcd: www.ks.uiuc.edu/Development/MDTools/catdcd/ Roland On Wed, May 15, 2013 at 3:14 AM, James Starlight wrote: > > Dear Gromacs users! > > I want to find possible way for the conversion of the set of the Gromacs's > xtc trajectories to the DCD format. > > The only possible w

Re: [gmx-users] g_cluster warning

Thanks for the report Sabine. It would be nice if the original reporters could take the extra 5 seconds to copy-paste and report the command lines they used. There are way too many things that they or GROMACS could be doing wrong for any of us to spend time guessing what is going on. :-) Mark O

[gmx-users] bending angle between 2 vectors defined by cm of groups of atoms

Dear users and experts, do you know if it is possible make the bending angle calculation in the following case? I have got three groups (G1, G2, G3) into a system. I have to define the center of mass of each one. I have to calculate the bending angle defined by vector 1 and vector 2. vector 1:

Re: [gmx-users] g_cluster warning

Hi, by looking into the code I could figure out some things. WARNING: rmsd minimum 0 is below lowest rmsd value 0.0247473 This warning comes from the -rmsmin option which is set to 0 by default and which controls the structure output. The problem with tpr/gro files is that g_cluster uses mass

Re: [gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

On 5/15/13 7:36 AM, aixintiankong wrote: i want to study how ligands change the conformations using the gromacs software and i want to run 100ns, but i don't konw how to reasonably set the nstxout nstvout nstenergy nstlog and nstxtcout. There is no universal answer. The main consid

Re: [gmx-users] simulate a protein covalently binding with a organic molecule

On 5/15/13 7:30 AM, aixintiankong wrote: Dear, Please help me . i want to simulate a systme of the protein covalently bind with a organic molecule. Part of the model is standard resides and the rest it is nonstandard(HETNAM) resides. The two parts covalently bind to each other. i don'

[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

i want to study how ligands change the conformations using the gromacs software and i want to run 100ns, but i don't konw how to reasonably set the nstxout nstvout nstenergy nstlog and nstxtcout. Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org http://lis

[gmx-users] simulate a protein covalently binding with a organic molecule

Dear, Please help me . i want to simulate a systme of the protein covalently bind with a organic molecule. Part of the model is standard resides and the rest it is nonstandard(HETNAM) resides. The two parts covalently bind to each other. i don't know how to get the topology of the model.

[gmx-users] simulate a protein covalently binding with a organic molecule

Dear, Please help me . i want to simulate a systme of the protein covalently bind with a organic molecule. Part of the model is standard resides and the rest it is nonstandard(HETNAM) resides. The two parts covalently bind to each other. i don't know how to get the topology of the model.

Re: R: Re: [gmx-users] range angle calculated by g_sgangle

On 5/15/13 3:50 AM, battis...@libero.it wrote: Dear Justin, thanks a lot for your reply that solve completely my problem. I would like signal that in the manual of g_sgangle there is no enough information about the three columns of the file sg_angle.xvg; furthermore the axis label into the fi

Re: [gmx-users] g_dist problem in Implicit solvent

Please keep the discussion on the mailing list. On 5/14/13 11:37 PM, Tong Li wrote: Hi Justin, Really appreciate your prompt reply! I got the inconsistence, the atom index in the original tpr file is different with the ones in xtc result file. However, I have no ideas what caused this… Some at

R: Re: [gmx-users] range angle calculated by g_sgangle

Dear Justin, thanks a lot for your reply that solve completely my problem. I would like signal that in the manual of g_sgangle there is no enough information about the three columns of the file sg_angle.xvg; furthermore the axis label into the file sg_angle.xvg is wrong. I suppose that this inf

Re: [gmx-users] Fwd: Static compilation of gromacs

On 15.05.2013 06:41, Андрей Гончар wrote: I know, but on target machine there is a gcc compilator version 4.1, and on gromacs site they told that this version is broken and 4.5 should used instead. So I try to compile it on machine with 4.5 version of gcc Андрей, if there is *no fftw3f on the t

Re: [gmx-users] Fwd: Static compilation of gromacs

В письме от 15 мая 2013 08:41:14 пользователь Андрей Гончар написал: > I know, but on target machine there is a gcc compilator version 4.1, and on > gromacs site they told that this version is broken and 4.5 should used > instead. So I try to compile it on machine with 4.5 version of gcc > You ca

[gmx-users] xtc2dcd conversion

Dear Gromacs users! I want to find possible way for the conversion of the set of the Gromacs's xtc trajectories to the DCD format. The only possible way that I know for such conversion is the VMD. But it's very routine for the big set of the XTC's inputs. Thanks for help, James -- gmx-users