=$PBS_O_WORKDIR export
NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'` export DIR=/work/rj/work_file
cd $DIR mpirun -machinefile $PBS_NODEFILE -np $NPROCS `which $EXEC` -nb gpu
-deffnm
bact
Hi there,
I have 24 threads in my PC with one GTX 980Ti GPU. I would like to run two
simulation job by assigning 12 threads for each job. I have tried using "-ntomp
12 -ntmpi 1" for mentioning the threads and gpu. However, i couldnt get the
similar speed as if run them alone with 12 threads.
Dear gmx,
I would like to calculate the H-bond occupancy between two residue (intra mol
inter Thr183 (OG1) -Tyr162 (N) ).
I made a .ndx file choosing the both atoms : Group40 ( r_162_&_N) has
1 elements
Group
Dear gmx,
I understand that probability distributions of distance can be calculated
through gmx analyze tool but how the probability distributions of others such
as SASA and secondary structure can be calculated?
Do i have to use other plotting tool R, gnuplot to do ? or can any gromacs
Dear all,
I have done protein with three different inhibitor for 100ns simulation and
would use the most populated structure for further analysis.
What i wonder is how do i select the perfect cut off value to choose the most
populated structure from 100ns? Is that following command can
Dear gmx,
I have a single PC contains 24 threads with GTX 980Ti.
I would like to know how do i run the 3 or 2 simulation in same time with above
mentioned PC would have similar speed. I also read about -pin options but
couldnt understand well. Moreover i run in default i get this error The
; charset=UTF-8
Hi RJ,
For an XTC file, you need to set nstxtcout (GMX 4.x) or nstxout_compressed
(GMX 5). A TPR file is a run _input_ file and is not generated as output.
Cheers,
Tsjerk
On Mon, Jun 22, 2015 at 6:11 AM, RJ ra...@kaist.ac.kr wrote:
Dear gmx.
I run 100ns simulation
Dear gmx.
I run 100ns simulation of my protein with ligand. After completing the 100ns,
the output doesnt give .xtc and .tpr files of final output. i could find .cpt
.edr .gro .tpr files of final output.
Please guide me how can i get the final output of these files ? Thanks
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Dear all,
I have a 64 bit PC with 16 processor with GTX460 gpu and wants to run multiple
simulation.
One simulation takes (~120 aa length) for 100ns about 4-5 days, whereas when i
subject same protein into 100ns, it shows it will take over a month to finish.
Is that any command that can
Dear gmx users,
I used gmx 5.0.4 for MD runs, and for the purpose of MMPBSA analysis ( only
compatible with 4.6 version) i used those files in gromacs 4.6 but end up with
errors:
By looking at the previous similar issues mail, i tried to make .tpr in gromacs
4.6 version but i couldnt able
Dear gmx users,
I tried DSSP of both binary and .exe by renaming it as dssp
(dssp-2.0.4-linux-amd64 dssp-2.0.4-win32.exe from
ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/) and placed in
usr/local/bin/dssp.
set the excusable too ( which dssp /usr/local/bin/dssp).
Both of them gives
Dear gmx
I have PC has 16 processor with GTX460 where i complied successfully by
following the gmx procedure.
When i run gmx mdrun, it does detects my gpu but i wonder whether its taking
for calculation or not ?
Here i get this info while running mdrun
Using 1 MPI thread
Using 16 OpenMP
RJ,
I think you need to inscribe 'source command' in your bash file.
In case of Ubuntu environment, If you insert 'source command' for
/etc/bash.bashrc, you can do use gromacs in all terminals without typing source
command.
You don?t need to set your PATH as you mentioned earlier.
Yoochan
Dear gmx,
I have installed the gmx in my ubuntu and centos system and tried to set the
environmental variable path in-order to use without mentioning the source
commend in my terminal of linux.
I tried to set my path as follows but couldn't success it.
export
Dear gmx,
I am simulation a kinase protein which has (~1200 aa) length. When I energy
minimize the protein with default em file from Justin A. Lemku tutorial. i have
got the following output.
writing lowest energy coordinates.
Steepest Descents converged to Fmax 1000 in 1162 steps
Dear gmx,
I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even
cleaned my crystal structure using Discovery studio/swissviewer which shows no
error on it. I wonder, how do i rectify this problem ?
WARNING: WARNING: Residue 1 named MET of a molecule in the input file was
-activation caused my
Mutant in protein?
Much appreciated for your valuable suggestion.
Regards
RJ
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Dear all,
How do i select different chain backbone in make_ndx ?
i could select the chain A and B desperately but cant select them together.
The manual says 'chain' ch1 [ch2 ..]
I tried as like the manual, but end up with error;
chain A | chain B r 236-297 | r 321-400 | r 433-512 | r
not open file:
topol.tpr
Dear Justin,
I already ran 10 ns without mentioned the energyrps. Now I have added the
energyrps in md.mdp file. Should i need to rerun 10 ns again to get the
interaction energies?
what does mdrun -rerun ?
On 2/13/15 7:07 AM, RJ wrote:
Dear all,
I need
to indicate the group of residues so?
Also, how do i calculate the interaction energies in nano second time scale (
seems there is no -tu option in gmx energy)?
Thanks
Regards
RJ
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Dear all,
Experimentally determined charges and non-bonded interaction values for ligand
atoms ( Written in charmm) can be used directly in gromacs provided charmm27.ff
? or does it need any conversion to use it in gromacs based charmm27.ff?
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