[gmx-users] Error:Cannot determine precision of trn file

Dear colleagues,   I successfully finished a 3 ns gromacs run using 40 nodes.  When, I tried to convert .trr file to .xtc using trjconv, the run stops at 560 frame giving error "cannot determimine precision of trn file". I tried various options like -skip, -b and -e, -dt option

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 32

thankyou Justin for your response. The gmxcheck output is as follows Reading frame 180 time  180.000   Reading frame 190 time  190.000   Reading frame 200 time  200.000 | | Distance between atoms 2208 and 2210 is 0.000, should be 0.136 Distance between atoms 2208 and 2209 is 0.000,

[gmx-users] Imposing distance restraints between two residues

Dear colleagues,     I want to impose simple distance constraint between the two ends of the same protein with missing residues in between. As I went through the manual I found I can use "constraints type 2" fixes the distance without connecting atoms by a chemical bond. Manual show

[gmx-users] Imposing distance restraints between two residues

Dear colleagues,     I want to impose simple distance constraint between the two ends of the same protein with missing residues in between. As I went through the manual I found I can use "constraints type 2" fixes the distance without connecting atoms by a chemical bond. Manual shows th

Re: [gmx-users] Imposing distance restraints between two

Dear colleagues,                   I thank Justin for your suggesting me the distance restraints.So, if I want to impose a distance restraint for 11.28 A between two atoms 4811 and 4812, I would include the following lines in the topology file. [distance_restraints] ;ai   aj     type index 

[gmx-users] Position restraints on a pentamer

Dear colleagues,    I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane domain. I am using "position restraints" for few of th

[gmx-users] Position restraints on a pentamer

Please ignore my previous mail. There was typo error. Dear colleagues,    I want to do MD simulation of only the extracellular domain of a pentamer, excluding the transmembrane domain. So, I want to restrain the part of the extracellular domain in contact with the transmembrane

[gmx-users] Bonds break while Minimising using distance restraints

Dear colleagues, I need to use simple distance restraints of 12.5 A between two CA atoms of two residues. I am using the following lines in the .itp file #ifdef DDISRES [distance_restraints] ;ai   aj type index type' low   up1  up2  fac 1703 1712 1    0 1    11.5  12.0 12.5 1.0 The first fe

[gmx-users] Re: Re: Bonds break while Minimising using distance restraints

[EMAIL PROTECTED] wrote: Hi Justin, thanks for your response. You are right. I get the following message in the .job file "Warning: 1-4 interaction between 6151 and 6160 at distance 1.387 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usu

[gmx-users] Re: Re: Bonds break while Minimising using distance restraints

Hi, There is no chance of steric clashes between 6151 & 6160. They are seperated by 12 A. ("Warning: 1-4 interaction between 6151 and 6160 at distance 1.387 which is larger than the 1-4 table size 1.000 nm. These are ignored for the rest of the simulation. This usually means your system is

Re: [gmx-users] Re: Re: Bonds break while Minimising using distance restraints

- Original Message - From: Ryogo Sugitani <[EMAIL PROTECTED]> Date: Wednesday, September 3, 2008 5:46 pm Subject: Re: [gmx-users] Re: Re: Bonds break while Minimising using distance restraints To: [EMAIL PROTECTED] > Latha, > > I'm not sure why there is 1-4 interaction between 6151 and

[gmx-users] Re: Bonds break while Minimising using distance restraints

Hi, The atoms are separated by 12 A (1.2 > nm). The atoms I restrained are 1703 & 1712 (6151 & 6160 atoms are also > from the same residues). These are the residues that looks as if they > are no bonds between them. ( residues alone, peptide bond alone and the > rest of the protein). How is it t

[gmx-users] Re: Bonds break while Minimising using solved

First of all I would like to thank Justin, for giving me a clue about checking the bonds in "chain_C.itp" file. When I removed all those unexpected bonds, minimization as successful. To summarize, I want to minimize a pentamer by imposing distance restraints in one of the chains. This chain has