[gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread nishtha pandey
Hello everyone, While trying to do the RMSD analysis of my trajectory file I am facing the error " Too many iterations in routine JACOBI". I have gone through the archives which suggests that such problem arises if there is mismatch between the reference structure and trajector

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread David van der Spoel
nishtha pandey wrote: Hello everyone, While trying to do the RMSD analysis of my trajectory file I am facing the error " Too many iterations in routine JACOBI". I have gone through the archives which suggests that such problem arises if there is mismatch between the refere

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread nishtha pandey
Hi, Thank you for your response. It is a protein molecule containing 610 amino acid residues. Thanks and regards, Nishtha On Sat, Jan 24, 2009 at 4:37 PM, David van der Spoel wrote: > nishtha pandey wrote: > >> Hello everyone, >> While trying to do the RMSD analysis of my

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread David van der Spoel
nishtha pandey wrote: Hi, Thank you for your response. It is a protein molecule containing 610 amino acid residues. you didn't answer my question. please inspect the molecular structure at the time point where the error occurs. Thanks and regards, Nishtha On Sat, Jan 24, 2009 at 4:37

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread nishtha pandey
Hello, The molecule is not planar it is 3D. Also I would like to mention that the same reference structure gave me result earlier. I chose protein as group for least square fit and CA for RMSD calculation. Thanks and regards, Nishtha On Sat, Jan 24, 2009 at 4:51 PM, David van der Spoel wr

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread David van der Spoel
nishtha pandey wrote: Hello, The molecule is not planar it is 3D. Also I would like to mention that the same reference structure gave me result earlier. I chose protein as group for least square fit and CA for RMSD calculation. Thanks and regards, try extracting the trajectory frame a

[gmx-users] Carbon tetrachloride

2009-01-24 Thread avinash kumar
Hello all, Does anybody have a .gro and .pdb containing carbon tetrachloride? I am having problems generating the .pdb as the conversion to gro is not taking place correctly? Thank you -- Avinash Kumar. ___ gmx-users mailing listgmx-users@gromacs.

Re: [gmx-users] Carbon tetrachloride

2009-01-24 Thread Justin A. Lemkul
avinash kumar wrote: Hello all, Does anybody have a .gro and .pdb containing carbon tetrachloride? I am having problems generating the .pdb as the conversion to gro is not taking place correctly? If you can describe what you are actually doing (i.e., commands you are issuing, etc), then

[gmx-users] CO2 Linear triatomic - topology problem

2009-01-24 Thread Eudes Fileti
Hi gmx-users, I am trying to build a CO2 topology. Because CO2 is a triatomic linear molecule there is a discontinuity in the potential for the angle of 180 degrees, so I must use virtual sites to circumvent the problem. I have create my topology (gave below) from arguments I read in the forum (htt

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread Tsjerk Wassenaar
Hi, On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey wrote: > Hello everyone, > While trying to do the RMSD analysis of my trajectory > file I am facing the error " Too many iterations in routine JACOBI". I have > gone through the archives which suggests that such problem ari

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

2009-01-24 Thread nishtha pandey
Hello, Thank you for your reply. I used .tpr file genarated from grompp for mdrun which generated the .trr file. I have not specified xtc-grps. Regards, Nishtha On Sat, Jan 24, 2009 at 11:02 PM, Tsjerk Wassenaar wrote: > Hi, > > On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey > wrote: > >

RE: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

2009-01-24 Thread Berk Hess
Hi, I just found out that I introduced a bug in 4.0.3, which could cause the pull code to crash or give wrong results when running single processor. In parallel it is correct. I committed fixed for 4.0.4. If you run in parallel things should be correct, or change in src/kernel/md.c: if (ir->

RE: [gmx-users] Segmentation fault preprocessing with pull_geometry = cylinder

2009-01-24 Thread Berk Hess
Hi, I found many bugs in the cylinder pulling code. I fixed them all for the upcoming 4.0.4 release. I now tested and checked everything properly and it should really be correct. If you want to use 4.0 now, check out the 4.0 release branch from cvs. Berk From: g...@hotmail.com To: gmx-users@gro

[gmx-users] reg: simulations in presence of electric fields

2009-01-24 Thread rams rams
Dear users, In the gmx manual it is mentioned that we can carry out the md simulations under electic fields (static I suppose). In the description under the title Electric Fields, it was described that number of cosines implemented is 1. What exactly it mean ?? The frequency is also 0. Does it mea

Re: [gmx-users] reg: simulations in presence of electric fields

2009-01-24 Thread David van der Spoel
rams rams wrote: Dear users, In the gmx manual it is mentioned that we can carry out the md simulations under electic fields (static I suppose). In the description under the title Electric Fields, it was described that number of cosines implemented is 1. What exactly it mean ?? The frequency

Re: [gmx-users] reg: simulations in presence of electric fields

2009-01-24 Thread rams rams
Thank you very much David. Ram. On Sat, Jan 24, 2009 at 3:36 PM, David van der Spoel wrote: > rams rams wrote: > >> Dear users, >> In the gmx manual it is mentioned that we can carry out the md >> simulations under electic fields (static I suppose). In the description >> under the title Electri

[gmx-users] Branched topology / Converting from psf

2009-01-24 Thread Roland Schulz
Hi, is there a smart way to build the topology (topol.top) for a branched polymer? In this case I try to build Lignin. The problem is that I need to apply a patch to each monomer depending on the connection and (as far as I understand) the termini databases are only applied to the end of a chain.