On Fri, Aug 30, 2013 at 11:18 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear Gromacs users,
I am analyzing the density of my spherical lipid vesicle using g_densmap
tool with the following options.
g_densmap -f vesicle_noPBC.xtc -s vesicle-12us.tpr -n index.ndx -dt 1000
-od -amax 6
Hello,
I am attempting to simulate a protein-ligand complex using distance
restraints to match it to NMR data.
The system runs stably without restraints. With restraints it tends to spit
out LINCS angle warnings and blow up under most conditions.
I'm attempting to use:
; Restraints
disre
From memory, the Bussi thermostat does take its seed from ld-seed. You
can see this yourself by observing that mdrun -reprod with ld-seed set
to some value of your choice is reproducible by itself and different
from that of a different ld-seed.
Mark
On Thu, Aug 29, 2013 at 9:15 PM, Ali Sinan
On Fri, Aug 30, 2013 at 8:56 AM, Trayder trayder.tho...@monash.edu wrote:
Hello,
I am attempting to simulate a protein-ligand complex using distance
restraints to match it to NMR data.
The system runs stably without restraints. With restraints it tends to spit
out LINCS angle warnings and
On Thu, Aug 29, 2013 at 9:54 PM, Albert mailmd2...@gmail.com wrote:
Hello:
I compiled 4.6.3 in HPC with following steps:
setenv OBJECT_MODE 64
/opt/cmake/2.8.9_new/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs/4.6.3
-DBUILD_SHARED_LIBS=OFF -DCMAKE_BUILD_TYPE=Release
But its not a xpm file. Its a dat file
On Fri, Aug 30, 2013 at 12:05 PM, Chandan Choudhury iitd...@gmail.comwrote:
On Fri, Aug 30, 2013 at 11:18 AM, Venkat Reddy venkat...@gmail.com
wrote:
Dear Gromacs users,
I am analyzing the density of my spherical lipid vesicle using g_densmap
tool
Thank you for your reply.
My box is quite small indeed, so my cut-offs are 0.5
If I make a single layer, I would have to run quite a small system in
z-direction.
My residue box size:0.62840 0.54421 1.6 0.0 0.0
-0.31420 0.0 0.0 0.0
My suspect of the
I think it is a dangerous practice to simulate with a cutoff of 0.5 nm.
Irrespectively of what you study.
Dr. Vitaly V. Chaban
On Fri, Aug 30, 2013 at 11:32 AM, Valentina valentina.erast...@durham.ac.uk
wrote:
Thank you for your reply.
My box is quite small indeed, so my cut-offs are 0.5
On 8/29/13 6:23 PM, Gianluca Interlandi wrote:
And interestingly, they point out at differences between the various
implementations of the switching function. Also, when trying to replicate the
CHARMM energies, the authors did not use any cutoff at all and performed the
calculations in vacuo.
Dear Justin,
Thank you very much, that works.
Regards,
Beng Hau
Date: Thu, 29 Aug 2013 08:01:10 -0400
From: Justin Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Creating an infinite sheet of graphene
To: Discussion list for GROMACS users
Hi,
As I know, g_spatial gives me the spatial distribution of a specified group. If
there is any tool to give me the planar distribution of group in x-y graph? Or
if there is any command to help me?
Thanks in advance for your help. I appreciate you.
Sincerely,
Shima
--
gmx-users mailing
On 8/30/13 11:18 AM, Shima Arasteh wrote:
Hi,
As I know, g_spatial gives me the spatial distribution of a specified group. If
there is any tool to give me the planar distribution of group in x-y graph? Or
if there is any command to help me?
g_densmap
-Justin
--
With what compiler? (e.g. consult mdrun -version) There are many known
bugs in early point versions of each minor release of gcc, for
example. This is why the installation instructions stress getting the
latest version of your compiler.
Otherwise, what is your .mdp file and simulation system
Hi Mark,
I have tried GCC 4.7.1, 4.7.2 and ICC 13 (with and without MKL, my
colleague also tried double precision) compilers, all showed the same
behavior.
I will add the .mdp file I have used but the problem consists for all input
files my colleagues tried (they had their own input files,
Hi,
I have been running some energy conservation tests with GMX4.6.3 and had
encountered some issues when using the AVX-256 instruction set.
I first noticed that my systems were freezing on a cluster that uses
Sandy-bridge CPUs and did not on a different cluster using SSE. After
realizing that
ewald_rtol of 1e-9 is a very long way from the normal range of values,
and your other electrostatics settings seem pretty normal. I'd expect
these results to be of doubtful value, but I am surprised to see
that/if there is a marked different with acceleration type. I suggest
you try a normal
Hi all,
I am trying to insert a water into a prosthetic group binding cavity. I
cant seem to get an output .pdb file of the insertions, I set GMX_TPI_DUMP
in my shell with $ export GMX_TPI_DUMP=xxx but no numbers seemed to work. I
cant really get good information out of the .xvg output either, it
Hi Mark,
Thank you for the suggestion, that's what I needed to know!
Best,
Ali Sinan Saglam
On Fri, Aug 30, 2013 at 3:51 AM, Mark Abraham mark.j.abra...@gmail.comwrote:
From memory, the Bussi thermostat does take its seed from ld-seed. You
can see this yourself by observing that mdrun
Dear Rafael,
Which version of GROMACS are you using? I cannot guarantee my following
comments are valid in 4.6.X, only on 4.0.X and 4.5.X.
What values have you tried from GMX_TPI_DUMP? Basically, the value you set
it to will be the energy value that will be compared with the epot of the
system
So I've added :
---
couple-moltype = Protein
couple-intramol = yes
---
and now I have non-zero dVcoul/dl, but the dVvdw/dl terms are still zero.
Why is this still zero/should I be concerned about that?
I'm also happy to no longer be seeing a 100% exchange rate (which I
Thanks for the reply João,
I am using gromacs 4.6.3, I did centre all 4 frames at the prosthetic
group.
I tried GMX_TPI_DUMP = 5.0e+3, 5.0e+20, and even 5.0e-03, still, not a
single .pdb file written.
I am doing this on a 4 frame trajectory, consisting of ~7000 atoms per
frame. I think it may have
PBC is on works, so the centering is not important. My question had to do
with the center of insertion: random for tpi, specific for tpic.
That's really my second guess, the infinite energies. The tpi code has a
way to deal with them internally. Run the insertion [mdrun] with -debug 1
flag and
I am centering the insertion on the prosthetic group, which I put as 0 0 0.
I have a 222 amino acid protein, in maybe .2 M NaCl, I parametrized flavin
mononucleotide, which sits inside the protein.
I got the .pdb files written, I was setting the GMX_TPI_DUMP in a different
terminal window. Dumb
Oh, you were talking about the Energy Distribution output (-tpid), sorry.
So, I haven't used much this output, but from what I see, that energies
histogram is going indefinitely. It seems like a bug in the calculation of
the energy bins, and my intuition is telling me that it has something to do
Sorry, where I said put it as the last coordinate on the .tpr file you're
building it should be put it as the last coordinate of each frame of the
.trr file. You'll need to do some trajectory hand-editing.
João
On Sat, Aug 31, 2013 at 2:41 AM, João M. Damas jmda...@itqb.unl.pt wrote:
Oh, you
Yes, I hand edited the .tpr file to get the thing to work, otherwise I got
errors with particle numbers being different.
On Fri, Aug 30, 2013 at 6:54 PM, João M. Damas jmda...@itqb.unl.pt wrote:
Sorry, where I said put it as the last coordinate on the .tpr file you're
building it should be
Thanks!
I will try these latest suggestions!
On Fri, Aug 30, 2013 at 7:27 PM, Rafael I. Silverman y de la Vega
rsilv...@ucsc.edu wrote:
Yes, I hand edited the .tpr file to get the thing to work, otherwise I got
errors with particle numbers being different.
On Fri, Aug 30, 2013 at 6:54
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