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
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
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
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
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
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
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.
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
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
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
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:
> >
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->
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
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
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
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
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.
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