Dear Gromacs user's,
Could anybody tell me how to calculate
energy autocorrelation function using Gromacs. I need it to take statistically
uncorrelated snapshots for further calculations or somebody has done the same
using some other method that is
Dear All,
I wanted to calculate configurational entropy of a protein by using g_covar
and g_anaeig as follows,
g_covar -f ../traj.xtc -s ../npt_prod -o eigenval -v eigenvec.trr -av
average.pdb
g_anaeig -v eigenvec.trr -entropy -temp 300
I got the following results
The Entropy due to the Quasi
Rather, find out what non-bonded scheme your models were parametrized to
use, and use that! These are often not free parameters!
Mark
On May 15, 2014 6:47 AM, sujithkakkat . sujithk...@gmail.com wrote:
Hello Justin,
I looked at the energy components. What I find is that Short Range LJ is
On 2014-05-15 09:07, tarak karmakar wrote:
Dear All,
I wanted to calculate configurational entropy of a protein by using g_covar
and g_anaeig as follows,
g_covar -f ../traj.xtc -s ../npt_prod -o eigenval -v eigenvec.trr -av
average.pdb
g_anaeig -v eigenvec.trr -entropy -temp 300
I got the
Dear Sir,
Thanks for the quick reply.
Using g_anaeig_d I've got both of them as 'nan'
The Entropy due to the Quasi Harmonic approximation is -nan J/mol K
The Entropy due to the Schlitter formula is nan J/mol K
Tarak
On Thu, May 15, 2014 at 1:30 PM, David van der Spoel
Dear gmx-users,
I’m having some problems trying to understand anomalous diffusion coefficient
values calculated with g_msd.
MSD was calculated for two box with a run of 100ns using these settings
integrator = md
tinit= 0
dt = 0.002
nsteps
Hi Yulian,
I've also faced the same problem. In different machine the value is coming
different.
Which method did you use to calculate entropy?
QH or Schlitter?
In my case Schlitter is giving 'nan'.
Did you solve your problem after then? If so, please suggest me how to deal
with this.
Tarak
Dear Sir,
Thank you again for guiding me towards this. Got some clue.
The g_anaeig code is
.
static void calc_entropy_qh(FILE *fp,int n,real eigval[],real
On 2014-05-15 11:40, tarak karmakar wrote:
Dear Sir,
Thank you again for guiding me towards this. Got some clue.
The g_anaeig code is
.
static void
Hello:
I try to submit Gromacs job with command:
mpirun -np 2 mdrun_mpi -s md.tpr -g -v
but it failed with messages:
--
It looks like opal_init failed for some reason; your parallel process is
likely to abort. There are
First, check your install of MPI works on a simple test program. Then,
check that GROMACS cmake picked up the MPI you expected, and that that's
really the one you're using at run time.
Mark
On Thu, May 15, 2014 at 3:28 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I try to submit Gromacs
On Thu, May 15, 2014 at 8:04 AM, ravikumarvenkatraman
ravikumarvenkatra...@gmail.com wrote:
Dear Gromacs user's,
Could anybody tell me how to
calculate energy autocorrelation function using Gromacs. I need it to take
statistically uncorrelated snapshots
Hello Mark:
thanks a lot for reply.
The MPI works fine in my machine when I run another problem.
How can I check whether gromacs cmake picked up the MPI that I expected?
I've already specified with options:
CMAKE_PREFIX_PATH=/soft/intel/mkl/include/fftw:/soft/openmpi-1.7.5
thx a lot
Part of the eigenval.xvg file
995 3.02979e-06
996 2.98051e-06
997 2.93131e-06
998 2.75594e-06
999 2.69955e-06
1000 2.56434e-06
1001 2.66401e-16
1002 1.43252e-16
1003 1.0735e-16
1004 8.0728e-17
1005 4.3465e-17
1006
On 5/14/14, 1:15 PM, Ali Khan wrote:
I just did. It turns out that when there is a charged lipid in the system
(as in my case), charmm-gui increases the effective concentration to
compensate for the system's net charge. I have pasted my discourse with
them below.
If this is the case, I
Try mdrun -version and have a look at the flags and stuff. Do a make
VERBOSE=1 and check the compile line doesn't refer to some other MPI.
Inspect the CMakeCache.txt in the cmake build directory.
Mark
On Thu, May 15, 2014 at 5:39 PM, Albert mailmd2...@gmail.com wrote:
Hello Mark:
thanks a
On 2014-05-15 19:20, David van der Spoel wrote:
On 2014-05-15 18:41, tarak karmakar wrote:
Hi Justin,
That's true and it is a C code and 0 index loop.
Then the strange jump 999 to 1000 came in to the picture.
But what about dealing with very small numbers?
What does g_covar print?
It seems
What does g_covar print?
It seems the problem might be there, because the jump by 10 orders of
magnitude in eigenvalue does not seem reasonable.
g_covar prints the following
Analysis is non-mass weighted
Fit is non-mass weighted
Diagonalized the 1386x1386 covariance matrix
Trace of the
Hi Everyone , I need some help . gromacs software is new for me . I want to
know how can I run my protein in presence of gold atoms . What force field
should be there that is compatible with gold atoms and what changes i need
to do .Is there any link that I can follow ? Please guide me .
Thanks
On 2014-05-16 06:03, tarak karmakar wrote:
What does g_covar print?
It seems the problem might be there, because the jump by 10 orders of
magnitude in eigenvalue does not seem reasonable.
g_covar prints the following
Analysis is non-mass weighted
Fit is non-mass weighted
Diagonalized the
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