Re: [gmx-users] solvent density around protein

g_sorient spits out, at the end, among other things, the average number of solvent molecules within the cutoff distance. To get the number of e.g. water oxygens within a given distance of a group of atoms on a per frame basis, you can use g_hbond -contact. Best, Matt 2009/4/6 Morteza Khabiri

Re: [gmx-users] density around protein

g_sorient returns the number of solvent molecules within a given distance range of a protein -- it may be what you are looking for. Matt 2009/4/5 Morteza Khabiri khab...@greentech.cz: Dear gmxusers I want to calculate the density of solvent around protein. I already tried the commands

Re: [gmx-users] How to show the created box?

package require pbctools pbc box should do it. On Sun, Feb 15, 2009 at 10:29 PM, Chih-Ying Lin chihying2...@gmail.com wrote: HI after creating the box, and write it into .gro file. when i try the .gro file with VMD, but the box is not shown. how can i show the created box with VMD?

Re: [gmx-users] pull code, lambda, and soft core availability

This seems to be a good reference for soft-core interactions. BEUTLER et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS. Chem Phys Lett (1994) vol. 222 pp. 529-539 On Thu, Feb 12, 2009 at 1:33 PM, chris.ne...@utoronto.ca wrote:

[gmx-users] g_sdf reference configuration question

2 is GLY C, Atom 3 is GLY CA; Atom 4 is Water OW. My question is, first, should I expect the GLY O to lie at the origin in all instances? Is this a bug, or user error? And if this is a bug, are the sdf data reliable? Regards, Matt --- Matt Wyczalkowski Doctoral Candidate, Biomedical Engineering

Re: [gmx-users] Concentration of Urea in urea solvation box

because of box size differences. Regards, Matt --- Matt Wyczalkowski Doctoral Candidate, Biomedical Engineering Pappu Lab: http://lima.wustl.edu Washington University in St. Louis On Thu, Sep 4, 2008 at 1:51 PM, [EMAIL PROTECTED] wrote: Hi All, This is a trivial question. But I am quite

[gmx-users] Visualizing g_sdf on a Mac

I'm looking into using g_sdf for analysis. The instructions suggest using gOpenMol: The output will be a binary 3D-grid file (gom_plt.dat) in the .plt format that can be be read directly by gOpenMol. However, the gOpenMol web site does not distribute Mac binaries (nor source). I am using Mac OS

[gmx-users] Corrupt TRR file -- skipping a bad frame?

, but I can't use that utility to extract the good data past the bad frame, since it dies at the bad frame. For what its worth, part1.trr from the original run was about 2.1Gb, and part1 + part2 are about 3.4Gb. Any ideas how I could recover good data in a TRR file past a bad frame? Regards, Matt

[gmx-users] Defining charges: [atomtypes] vs [atoms]

Looking through the documentation, it seems like the charge of an atom may be defined in one of two ways: in the [atomtypes] directive, or in the [atoms] directive. In the past, I've always made them identical, but I have seen examples where they differ. Why are there two ways to define an

Re: [gmx-users] regarding range checking error and constraint errors in Lincs algorithm

-- Matt Wyczalkowski Doctoral Candidate, Biomedical Engineering Pappu Lab: http://lima.wustl.edu Washington University in St. Louis [EMAIL PROTECTED] ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Scaling Coulomb interactions with lambda, on a pair-wise basis

. Is there a way to scale Coulomb interactions for a specific pair of atoms only? Thanks in advance -- Matt -- Matt Wyczalkowski Doctoral Candidate, Biomedical Engineering Pappu Lab: http://lima.wustl.edu Washington University in St. Louis [EMAIL PROTECTED