Dear Users,
I have encountered a problem that mdrun always crashes with the following
msg, when I run it on more than 32 nodes:
Software inconsistency error:
Limiting the number of GPUs to 1 doesn't make sense (detected 1, 0
requested)!
For more information and tips for troubleshooting, please
On 3/27/15 4:05 AM, Priya Das wrote:
The following is the attached pose.str file.
1) Does param penalty or charge penalty matters?
Yes.
2) How do we know that the list does not accept attachments?
It's something I say weekly, if not more often. It should also have been in the
welcome
The following is the attached pose.str file.
1) Does param penalty or charge penalty matters?
2) How do we know that the list does not accept attachments?
3) I am following the tutorial for validation of penalties. As CHARMM is
not free cannot download it. So using Accelry's Discovery Studio
Thank you for your prompt reply, Abhijit.
I removed all the hydrogen atoms in arm.gro, and changed the number of
atoms from 560 to 520, then run the command
gmx x2top -f arm.gro -o top.top -ff cnt_oplsaa
and, unfortunately, segmentation fault again.
It seems that in previous versions (4.6.7
Dear users,
If I want to calculate distance of each residue's COM of a protein to a
surface is g_mindist going to be my friend? It is documented that
g_mindist computes the distance between one group and a number of other
groups. Both the minimum distance and the number of contacts within a given
Granted, the previous parameter set I referenced, I found in under 2 minutes of
searching, there was a paper in 2001 (see below) that discusses OPLS parameters
for nucleic acids. The authors of that paper may have some better idea of where
to find newer versions.
J. Pranata; S. G. Wierschke;
Hi,
I have looked at your carbon nanotube coordinate file (arm.gro). There the
terminal C atoms are hydrogen terminated. But you
modified the ffnonbonded.itp file with only C atoms. You need to add the
parameters for H atoms also both in ffnonbonded.itp and
atomname2type.n2t file. Hope this will
On 3/27/15 7:47 AM, Hao Ren wrote:
Hi there,
I am trying a MD simulation for carbon nanotubes, but encountered a problem
in the preparation of topology file.
The coordinates and modified force filed can be found here:
https://www.dropbox.com/s/qv4j33sivn56iey/test_x2top.tgz?dl=0
I prepared
Hi there,
I am trying a MD simulation for carbon nanotubes, but encountered a problem
in the preparation of topology file.
The coordinates and modified force filed can be found here:
https://www.dropbox.com/s/qv4j33sivn56iey/test_x2top.tgz?dl=0
I prepared the modified OPLS/AA force filed as
On 3/27/15 8:03 AM, James Lord wrote:
Dear users,
If I want to calculate distance of each residue's COM of a protein to a
surface is g_mindist going to be my friend? It is documented that
g_mindist computes the distance between one group and a number of other
groups. Both the minimum distance
If the earlier versions generate the topology then I guess the problem is
in your installation.
I can't help you much in this regard cause I never tried g_x2top in gromacs
5 version.
Thanks
Abhijit
On Fri, Mar 27, 2015 at 6:11 PM, Hao Ren renh...@gmail.com wrote:
Thank you for your prompt
I just used the topology file generated by g_x2top 4.6.7 to solvate the
system with my 5.0.4 installation
==
gmx solvate -cp arm.gro -p top.top -o arm_solvated.gro
==
and succeed.
I also succeed in several test simulations, such as Dr. Lemkul's tutorials
I, II and III using my 5.0.4
Hi Justin Lemkul,
Thank you very much for the reply. I have tried using
x2top for generating topology. I copied contents of opls ff to poly ff and
added some atoms and ran the command. The output was as follows:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman
On 3/27/15 9:25 AM, sridhar dwadasi wrote:
Hi Justin Lemkul,
Thank you very much for the reply. I have tried using
x2top for generating topology. I copied contents of opls ff to poly ff and
added some atoms and ran the command. The output was as follows:
GROMACS is written
Hi Chungwen,
I run on Piz Daint on a regular basis and never had these issues. The
only reason for such a thing to happen is that some strange rank over
nodes distribution ends up leaving some nodes without PP rank.
Could you please post a log file (thread pastebin or something
similar) of the
Thank you Justin for conforming this. /ren
On Fri, Mar 27, 2015 at 9:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/27/15 7:47 AM, Hao Ren wrote:
Hi there,
I am trying a MD simulation for carbon nanotubes, but encountered a
problem
in the preparation of topology file.
The
Hi,
That is not the full output, please share the *full* stderr/stdout
(and don't paste it into the mail body, please). I find it hard to
believe that the log is completely empty, if the application does
actually start up, at least the version header should be present in
the log file.
That your
Hello Szilárd,
Thanks for your response. The error msg I got:
from the slurm report:
Rank 31 [Tue Mar 10 15:50:53 2015] [c6-2c0s5n2] application called
MPI_Abort(MPI_COMM_WORLD, -1) - process 31
Rank 27 [Tue Mar 10 15:50:53 2015] [c6-2c0s4n2] application called
MPI_Abort(MPI_COMM_WORLD, -1) -
On 3/27/15 2:17 PM, marziyeh poshteh shirani wrote:
Hi all
I have the following error and I could not solve it after checking all
the possible solutions on line.
Thank you
M.P.Shirani
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernaktoppush.c, line: 1166
Hi Justin,
Thanks,
g_dist is calculating the centre of mass of two groups and -dist option
print all atoms in group 2 closer than dist to
the centre of mass of group 1, while what I am looking after is the
distance of COM of residues to a surface not the centre of mass of the
surface. Am I missing
On 3/27/15 4:14 PM, James Lord wrote:
Hi Justin,
Thanks,
g_dist is calculating the centre of mass of two groups and -dist option
print all atoms in group 2 closer than dist to
the centre of mass of group 1, while what I am looking after is the
distance of COM of residues to a surface not the
Hi all
I have the following error and I could not solve it after checking all
the possible solutions on line.
Thank you
M.P.Shirani
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernaktoppush.c, line: 1166
Fatal error:
Atomtype CH2 not found
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