Re: [gmx-users] dumping energies

Ryan Day wrote: Hello, I am trying to get the energies of individual waters in a trajectory. I am currently using an index file that defines each water individually, but, since I have ~9000 waters and can only define 254 energygrps at a time, this gets ugly quickly. I found some discussion in t

[gmx-users] dumping energies

Hello, I am trying to get the energies of individual waters in a trajectory. I am currently using an index file that defines each water individually, but, since I have ~9000 waters and can only define 254 energygrps at a time, this gets ugly quickly. I found some discussion in the list archices a

Re: [gmx-users] measure of radius of cytochrome c

try g_gyrate serge Taeho Kim wrote: Hello. Is there anybody to know the method how to measure of radius of molecules something like cytochrome c? ___ gmx-users mailing list

Re: [gmx-users] genion in gromacs 3.3.1

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 > >> You can try -norandom. I was under the impression that the potential >> based placement was broken (had been for a while). > > Hi David, Thank you very much, the command line option -norandom did work and placed the cations in the same place as

Re: [gmx-users] genion in gromacs 3.3.1

Miguel Ortiz Lombardia wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear colleagues, It looks like genion behaviour has changed in gromacs 3.3.1 as compared to 3.3 I still have both binaries in my machine and when using identical inputs to add some Na cations the new one (3.3.1) adds t

[gmx-users] genion in gromacs 3.3.1

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear colleagues, It looks like genion behaviour has changed in gromacs 3.3.1 as compared to 3.3 I still have both binaries in my machine and when using identical inputs to add some Na cations the new one (3.3.1) adds them randomly, while the previous

[gmx-users] Re: Problems with x2top

Steven Kirk wrote: Hello David, I am having some major problems with x2top. I have a PDB file containing atomic coordinate data for a silica nanoparticle, which I want to convert to a valid topology using the OPLS-AA force field. Using the latest version of GROMACS (3.3.1), I tried the x2top

Re: [gmx-users] (no subject)

caterina merla wrote: Hallo to all I try to use the function g_dielectric but it does not work , before I use the function g_dipoles to create the ACF of the all system it is the dipcorr.xvg and I put it as the input file for the g_dielectric but I obtained a message of error, I 'd like to k

[gmx-users] (no subject)

Hallo to all I try to use the function g_dielectric but it does not work , before I use the function g_dipoles to create the ACF of the all system it is the dipcorr.xvg and I put it as the input file for the g_dielectric but I obtained a message of error, I 'd like to know which is the co

[gmx-users] (no subject)

Hallo to all I try to use the function g_dielectric but it does not work , before I use the function g_dipoles to create the ACF of the all system it is the dipcorr.xvg and I put it as the input file for the g_dielectric but I obtained a message of error, I 'd like to know which is the corre

Re: [gmx-users] measure of radius of cytochrome c

Taeho Kim wrote: Hello. Is there anybody to know the method how to measure of radius of molecules something like cytochrome c? First, define what you mean by radius. Then work out how to calculate it. Then look for a tool to do that (crudely, you could do it using a visualization program),

Re: [gmx-users] measure of radius of cytochrome c

Taeho Kim wrote: Hello. Is there anybody to know the method how to measure of radius of molecules something like cytochrome c? try g_gyrate note however that the radius is dependent on what definition you choose to use. --

[gmx-users] measure of radius of cytochrome c

Hello. Is there anybody to know the method how to measure of radius of molecules something like cytochrome c? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests

Re: [gmx-users] hi

> hi today i have tried to run the position restrained dynamics using my tpr > file > grompp -f pr.mdp -c 7/trp_b4pr.gro -p 1/trp.top -o 8/trp_pr.tpr > > But its showing the error > Fatal error: > number of coordinates in coordinate file (7/trp_b4pr.gro, 14580) > does not match topo

[gmx-users] hi

hi today i have tried to run the position restrained dynamics using my tpr file grompp -f pr.mdp -c 7/trp_b4pr.gro -p 1/trp.top -o 8/trp_pr.tpr But its showing the error Fatal error: number of coordinates in coordinate file (7/trp_b4pr.gro, 14580) does not match topology (1/trp.top,