On 2/27/14, 2:03 AM, Francesca Vitalini wrote:
Residue 2 is just alanine,the most standard amino acid ever.
What Gromacs version is this? Is ACE correctly listed in residuetypes.dat as a
protein residue? pdb2gmx will also tell you this if it warns that residue 1 and
2 are not of the
Dear Dr,
Which details or files do you need? I would be very happy to solve this
question by posting any kind of files that you request.
2014-02-23 22:21 GMT+01:00 Dr. Vitaly Chaban vvcha...@gmail.com:
You do not provide all the details. As was pointed at the very
beginning, most likely you
Hi Justin
The bilayer is full solvated. It has 128 ceramide and 5120 water molecules
(40 water molecule per ceramide).
I ran same simulation on my desktop machine it is working properly,
properties such as potential energy and area per lipid converse very nicely.
Is there any problem with
thanx Dr. Vitaly
could you please explain me what did you mean by incorrectly treating of
periodicity? Is it related to update of neighbour list? My system is
periodic in 3 dimension and pressure coupling is anisotropic.
--
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On 2/27/14, 8:32 AM, gupta.rakesh082 wrote:
Hi Justin
The bilayer is full solvated. It has 128 ceramide and 5120 water molecules
(40 water molecule per ceramide).
I ran same simulation on my desktop machine it is working properly,
properties such as potential energy and area per lipid
Hi Gupta, :
Is there any problem with server or running on multiple thread.
your system seems to be very small and is probably subject
to strong fluctuations in pressure and/or energy. Could
you please create two directories containing (only) the
- mdp file for input (your md.mdp)
- topology
Hi,
Thanks for the report. In relation to
https://gerrit.gromacs.org/#/c/2726/I had been planning to add some
tests for the actual algorithm used, and
this report made me prioritize this. Here's an intermediate result. I have
not yet tested the PBC-enabled computation at all, and haven't looked
I am using Gromacs 4.5.5. In my residuetypes.dat ACE is correctly listed as
protein residue and pdb2gmx doesn't give any error about protein type.
For clarity I copy here my pdb, the interesting parts of the aminoacids.rtp
file and the pdb2gmx command.
Thank you very much for any help you can
I am using Gromacs 4.5.5. In my residuetypes.dat ACE is correctly listed as
protein residue and pdb2gmx doesn't give any error about protein type.
For clarity I copy here my pdb, the interesting parts of the aminoacids.rtp
file and the pdb2gmx command.
Thank you very much for any help you can
On 2/27/14, 9:48 AM, Francesca Vitalini wrote:
I am using Gromacs 4.5.5. In my residuetypes.dat ACE is correctly listed as
protein residue and pdb2gmx doesn't give any error about protein type.
For clarity I copy here my pdb, the interesting parts of the aminoacids.rtp
file and the pdb2gmx
The only real way to troubleshot this kind of problems is that someone
here starts your system at his local PC and sees the problem by the
own eyes.
As no one confirmed the same issue as yours, it is most likely that
the cause of problem lies outside gromacs code. Either something is
wrong with
Hi,
On Thu, Feb 27, 2014 at 4:09 PM, Teemu Murtola teemu.murt...@gmail.comwrote:
I'll post additional information once I have had time to test more cases.
I have now created http://redmine.gromacs.org/issues/1445 to track the
issue, and uploaded a fix to Gerrit:
Please make sure to use the OpenMPI cygwin package 1.7.1-2
When I installed the latest upgrade, MPI troubles occurred and Gromacs mdrun
was broken.
Details:
The troubles were:
1) MPI installation was no longer detected by cmake (when I tried rebuilding)
2) could no longer execute mpirun nor
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