[gmx-users] relative constraint deviation after lincs

hi users, I want to simulate a position restraint md. pdb2gmx creates a correct protein.top and a posre.itp file. but when I use " define = -DPOSRES" I have this error: Step 1004, time 2.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.026978, max 1.366297 (between atoms

Re: [gmx-users] 3Dplot

David van der Spoel ha scritto: Alessandro Casoni wrote: Dear gmx-users, i would like to generate a 3D plot of my potential energy/RMSD/radius of gyration. I used g_energy, g_rms and g_gyrate to collect informations on my simulation..any suggestion on software able to generate 3D plot

[gmx-users] 3Dplot

Dear gmx-users, i would like to generate a 3D plot of my potential energy/RMSD/radius of gyration. I used g_energy, g_rms and g_gyrate to collect informations on my simulation..any suggestion on software able to generate 3D plot? thanks alessandro

[gmx-users] ResNumber in PDB2GMX

Hello users, i have just a simple question.. ..when I create a *.gro file starting from a PDB structure the numbers of residues start from 1 in the output file,even if in my initial protein the sequence start from another number.. Any suggestion to renumber correctly my output file? best r

Re: [gmx-users] Re: how to show dodecahedron box in VMD

Tsjerk Wassenaar ha scritto: Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: Dear all: I am trying to show the dodecahedron box only in vmd since my simulation box is dodecahedron. If

Re: [gmx-users] bad box in protein.gro

rhombic dodecahedon in Chapter 3 of the manual). Cheers, Tsjerk On 11/10/08, Alessandro Casoni <[EMAIL PROTECTED]> wrote: Hi all, when i use "editconf" to generate a dodecahedron box with the command: editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9 the out

[gmx-users] bad box in protein.gro

Hi all, when i use "editconf" to generate a dodecahedron box with the command: editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9 the output show me the following message: . WARNING 1 [file aminoacids.dat, line 1]: Bad box in file protein.gro Generated a cubic box6.941 x

Re: [gmx-users] Problem building a new polymer using pdb2gmx....

Alberto Sergio Garay ha scritto: Dear users I'm trying to build a polymer with a new building block. I have included the new topology block inside the force field rtp file, which I've choosen for my simulation (ffG53a6.rtp). I've also prepared a gro input file, where the atoms of each residue

Re: [gmx-users] Magic Number Error

stop..i found this in the log file: Step Time Lambda 688000 1376.00012 0nul>... Il giorno lun, 28/01/2008 alle 12.26 +0100, alessandro casoni ha scritto: > well, I generated xtc file on a different system..but other files > generate in the same way appear

Re: [gmx-users] Magic Number Error

well, I generated xtc file on a different system..but other files generate in the same way appear to be ok.. The size is correct.. Il giorno lun, 28/01/2008 alle 21.51 +1100, Mark Abraham ha scritto: > alessandro casoni wrote: > > Dear GMX-USERS, > > I have a little problem...when

[gmx-users] Magic Number Error

Dear GMX-USERS, I have a little problem...when I use g_covar I get this message: Program g_covar, VERSION 3.3.2 Source code file: xtcio.c, line: 83 Fatal error: Magic Number Error in XTC file (read 0, should be 1995) ..could you help me? thanks in advance Alessandro __