[gmx-users] Re: viscosity and acflen in g_energy

Mark, In "g_energy -h" I see nothing abous viscosity except the option "-vis". The command line is as I wrote earlier: "g_energy -vis -acflen 1001" The system is liquid water. The simulation time is 2 000 ps. The file I look into is enecorr.xvg. What the error of some sort do you mean? Vitaly

Re: [gmx-users] Static build

I'm trying to find a package that distributes libSM.a On Sat, Sep 26, 2009 at 10:39 PM, Mark Abraham wrote: > Jack Shultz wrote: >> >> Hello, >> >> I am trying to build statically with the small source changes I made >> yesterday. >> >> I'm building on 32 bit linux with single precision. I have l

Re: [gmx-users] trjconv => not get the enough data ?

Chih-Ying Lin wrote: Hi in my .mdp file, i set up the total 4000 times saving the coordinates of each atom. then, I use the command trjconv -f xx.gro -s xx.tpr -o xx-traj.gro then, i checked the xx-traj.gro file and found there were less than 4000 times of recording coordinates for each a

[gmx-users] trjconv => not get the enough data ?

Hi in my .mdp file, i set up the total 4000 times saving the coordinates of each atom. then, I use the command trjconv -f xx.gro -s xx.tpr -o xx-traj.gro then, i checked the xx-traj.gro file and found there were less than 4000 times of recording coordinates for each atom. say 3600 times of

Re: [gmx-users] Problem with domain decomposition

Stephane Abel wrote: Hi gromacs users and experts I am doing some simulations using 8 CPU of solvate peptide (8 AA) in octahedron truncated box (5150) with SPC water with GMX 4.05. To simulate during a long time i am cutting my simulation in 24 h time period (25 ns/day) using checkpoints

Re: [gmx-users] viscosity and acflen in g_energy

Vitaly V. Chaban wrote: Hi, When using g_energy to calculate viscosity ("g_energy -vis"), in enecorr.xvg the ACF of stress tensor is output. How can one specify the "acflen" of this ACF? I try the key "g_energy -vis -acflen XXX" but the length of the ACF is still equal to the half of the traject

Re: [gmx-users] Static build

Jack Shultz wrote: Hello, I am trying to build statically with the small source changes I made yesterday. I'm building on 32 bit linux with single precision. I have libSM [r...@vps gromacs-4.0.5]# ls /usr/lib/libSM* /usr/lib/libSM.so /usr/lib/libSM.so.6 /usr/lib/libSM.so.6.0.0 I get this er

Re: [gmx-users] Re: Re: Re: umbrella potential

Stefan Hoorman wrote: Well, I tried again, this time simulating 1ns each window. I thought about simulating more, but thought of making a test before making longer simulations for nothing. And again, my histogram looks like a chromatographic peak, but the range this time is different. The re

[gmx-users] Re: Re: Re: umbrella potential

> Stefan Hoorman wrote: > > > I simulate 400 ps for each window. I have a total of 20 windows. My > > 400 ps is relatively short, especially given the speed of current hardware > and > of Gromacs 4.0. I generally see longer time periods in the literature. > > > histogram looks like a chromatograph

Re: [gmx-users] computing dihedral given 4 atoms

ok, just realized that -ov option of g_angle gives the values for each frame. ignore my previous mail. Rgds Sandeep On Sat, Sep 26, 2009 at 6:32 PM, sandeep somani wrote: > Hi Justin > > I had missed the -type flag of g_angle. > > But it gives the distribution of the dihedral, not the value c

Re: [gmx-users] computing dihedral given 4 atoms

Hi Justin I had missed the -type flag of g_angle. But it gives the distribution of the dihedral, not the value corresponding to each frame. for example, g_angle_d -f mol.xtc -n torsion.ndx -type dihedral followed by selection of a group with 4 atoms generated one output file angdist.xvg which l

Re: [gmx-users] computing dihedral given 4 atoms

sandeep somani wrote: hi I have simulated a molecule (not a standard protein) with gmx and now need to compute dihedral angles between specified atoms for all frames of in the .xtc file. Is there any utility along the lines of g_bond whcih computes the dihedral/torsion angle given 4 atom

[gmx-users] computing dihedral given 4 atoms

hi I have simulated a molecule (not a standard protein) with gmx and now need to compute dihedral angles between specified atoms for all frames of in the .xtc file. Is there any utility along the lines of g_bond whcih computes the dihedral/torsion angle given 4 atom numbers in a index file group

[gmx-users] How does g_fg2cg work?

Dear GMXers, Is there anybody who use the g_fg2cg routine for mapping and reverse-mapping coarse-grained model on all-atom model? I want to know how it works, i.e. whether is the center of mass of a group of atoms used as superatom? How is the atomistic detail reintroduced to coarse-grained

Re: [gmx-users] Trajectory files in vmd

Aditi Borkar wrote: Dear Rui, Thanx for the explanation. I did not know that VMD only calculates the secondary structure fort he first frame only. Is there an option to calculate the secondary structure (say in New cartoon representation) of all the frames in the trajectory? You can use th

[gmx-users] Bug in g_chi -p?

Hi, I'm trying to calculate order parameters from g_chi for a protein complex with bound ligand. I'm using version 4.0.5, and if I specify the -p option, the program gives a Bus error without writing all the output: g_chi -s ./0_10ns/md_0_10.tpr -f fix_400.xtc -o -jc -g -p ... 130 residue

Re: [gmx-users] 1-4 interactions

You can either specify this explicitly or use the fudge LJ and fudge q headers in your topology file. See the manual for details. On Sep 26, 2009, at 1:51 AM, Vitaly V. Chaban wrote: Hi, Is it possible in gromacs to make 1-4 interaction energy reduced as compared to the intermolecular inter