sampling
actually reduces. I'm not aware of anybody who's actually done that - but
it would certainly be an advantage if your application is interested in
data at a range of temperatures.
Mark
On Fri, May 17, 2013 at 11:10 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Histograms 101
?
top2psf has no idea what to do with this file, by the
way.
Would it help for me to provide the pre-processed and post-processed top
files?
Sure, but attachments will generally be rejected. Use a file sharing
service.
Mark
Cheers,
David
On Fri, May 17, 2013 at 10:17 AM, Mark Abraham
On Fri, May 17, 2013 at 10:21 PM, Shima Arasteh shima_arasteh2...@yahoo.com
wrote:
Hi,
I am simulating a system composed if POPC , peptide, waters and ions.
I used the InflateGRO methodology to construct the system.
There are 2 phenylalanine residues in my peptide. Each phenyl has 2rings
Cray's compiler is largely/wholly untested. I'd suggest you use the version
of gcc that you know works.
For use on a big cluster, you probably don't want Thread MPI anyway. Does
cmake -DGMX_MPI work?
Mark
On Sat, May 18, 2013 at 12:01 AM, Humayun Arafat hasa...@gmail.com wrote:
Hi,
I need
On Thu, May 16, 2013 at 2:04 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Dear Sir,
Here's the result of three different runs :
Temperature distribution for three trials
Repeat-1 280 298 317 337 359 382 406 432 460 489 520 554 589 627
Repeat-2 280 299 319 340 363 388 414 441 471 503
Does manual 2.3 help?
On Thu, May 16, 2013 at 2:51 PM, Rasoul Nasiri nasiri1...@gmail.com wrote:
Hi All,
Has anyone performed MD simulation on fluids in reduced units with GROMACS?
I just wandering how the obtained density values through the box should be
converted in the SI unit (Kg/m3).
1023457896 10 11 12
8 2013468795 10 11 12
10 3012578694 11 10 12
On Thu, May 16, 2013 at 11:24 PM, Mark Abraham mark.j.abra...@gmail.com
wrote
On Thu, May 16, 2013 at 12:37 PM, Alan alanwil...@gmail.com wrote:
With ACPYPE I can convert any Amber *.prmtop and *.crd to Gromacs, but it
doesn't mean it will work straightforward (but I am working for that).
For example, I am wondering how Gromacs team will port the Amber FF12SB,
cmake -DGMX_THREAD_MPI=on is intended to provide maximum performance for
your case, i.e. a single node. It's on by default for a reason ;-)
Mark
On Thu, May 16, 2013 at 6:57 PM, Thomas Schlesier schl...@uni-mainz.dewrote:
Dear all,
if one performs a parallel calculation on a single node /
assumed this was mercury!
So I'd strongly advise everybody to use tpr files within g_cluster. It
would also be nice to insert a warning in g_cluster if atoms other than C,
O, N, H, S are found.
Cheers
Sabine
On 05/14/2013 06:06 PM, Mark Abraham wrote:
Hi,
I don't know. I don't know how
We'd need a lot more info to start to understand why .tpr vs .gro
does/should affect the result (or not)!
Mark
On May 14, 2013 2:32 PM, Sabine Reisser sabine.reis...@kit.edu wrote:
Hi,
I'm having the same warning, would also be interested in what it means.
Additionally, I get different
Hi,
I don't know. I don't know how to trigger it, and nobody has said how they
triggered it :-)
Mark
On May 14, 2013 4:45 PM, Preeti Choudhary
preetichoudhary18111...@gmail.com wrote:
should we worry about the warning ???
On Tue, May 14, 2013 at 7:19 PM, Mark Abraham mark.j.abra
I wouldn't call 8ps late. Since you probably don't know how large a time
step is safe, I'd try 0.1 fs for equilibration, and raise it later if it
proves stable.
Mark
On May 14, 2013 4:28 PM, Joe Smerdon jsmer...@uclan.ac.uk wrote:
Hi all,
First of all I'm new to md simulations, so if I am
Try selecting residue 0 with editconf and see for yourself :-)
On May 14, 2013 4:41 PM, gromacs query gromacsqu...@gmail.com wrote:
Dear Nuno,
I used genconf -f del.gro -o del.g96
Again it gives max of 9 then starts with 0; sample shown here
del.g96
9 SOL OW332114
On Sat, May 11, 2013 at 2:07 AM, salehi sal...@umich.edu wrote:
I was trying to install gromacs 4.6.1 with CUDA and have a weird problem.
My system is as the following
new iMAC OS x 10.8.3
GPU : FTX 650 M 512 MB
I also installed the open-mpi libraries into the /usr/local/lib folder
before
On Sat, May 11, 2013 at 5:15 AM, Christopher Neale
chris.ne...@mail.utoronto.ca wrote:
The lack of line-wrapping makes it a pain to read. It happens to my emails
that are posted on this list
(and I have seen others), unless I put explicit line-breaks in my posts,
which I often forget to do.
Refs 11 and 12 from section 4.9.2 of the manual have the kind of content
you are seeking, IIRC.
Mark
On Sat, May 11, 2013 at 7:29 PM, Andrew DeYoung adeyo...@andrew.cmu.eduwrote:
Hi,
Please forgive me for this slightly off-topic question. Suppose I use the
particle mesh Ewald algorithm
for sure is a bit of an overbid :) If the overall cost is dominated by
computation over the range of N of interest, then the scaling properties of
the computation will dominate the overall scaling.
Mark
On Sat, May 11, 2013 at 8:15 PM, francesco oteri
francesco.ot...@gmail.comwrote:
Hi
On Mon, May 6, 2013 at 3:48 AM, Kong xq xqkong...@gmail.com wrote:
Hi Mark,
Thanks for your great help. I am sorry for the negligence to state the
variation value correctly( it should be 0.011 rather than 0.11). Does this
somewhat small value indicate the generalized equilibrium achieved?
On Sun, May 5, 2013 at 8:12 PM, Martin Siegert sieg...@sfu.ca wrote:
Hi,
On Sat, May 04, 2013 at 09:50:37AM +0200, Mark Abraham wrote:
On Sat, May 4, 2013 at 1:41 AM, Martin Siegert sieg...@sfu.ca wrote:
Hi,
I am struggling with the configuration and compilation/installation
On Sun, May 5, 2013 at 5:14 PM, Kong xq xqkong...@gmail.com wrote:
Dear GMX users,
I have some concerns about the statistics analysis of REMD which do
need your generous help.
I performed a 50ns isothermal-isobaric REMD simulation with 64 replicas
spaning from 300K to 390K. Then I
On Sat, May 4, 2013 at 1:41 AM, Martin Siegert sieg...@sfu.ca wrote:
Hi,
I am struggling with the configuration and compilation/installation
of gromacs-4.6.1. Our cluster has 2 different processors: the older
generation supports sse4.1, the newer sse4.2. Configuration and
compilation must
Trajectory frames written by mdrun are not post-processed to guess how you
would like PBC to be treated for whatever purpose you have next. So if a
molecule straddles a periodic boundary given the current center position,
that's what it looks like. If there are things you want to do, then there's
gen_vel controls the generation of random velocities. grompp follows it
(but I'd have to check the code to see what it does if you use grompp -t).
tprconv does not follow it.
The random seed is in a different variable, but only does anything if
gen_vel=yes.
I am not sure what the basis of your
, but there
are countless other points where the code may or may not still be doing
something that was correct at some point in the last 15 years under certain
assumptions, but may not be correct now or under new conditions...
Mark
2013/5/3 Mark Abraham mark.j.abra...@gmail.com
Trajectory frames
with
the pre-EM velocities (even if it is possible, which I do not think it
should be). The energy distributions are guaranteed to be mutually
inconsistent.
Mark
James
2013/5/3 Mark Abraham mark.j.abra...@gmail.com
On Fri, May 3, 2013 at 11:15 AM, James Starlight jmsstarli...@gmail.com
wrote
On Fri, May 3, 2013 at 3:17 PM, James Starlight jmsstarli...@gmail.comwrote:
Mark,
but if I run npt equilibration onto minimized structure (without
velocities) without definition of the new velocities in the npt.mdp file
gen_vel = No
I noticed that in npt.gro file velocities present.
Were you using the 4.6.1 regression test package?
Mark
On May 3, 2013 7:53 PM, José Luis Gordillo Ruiz j...@super.unam.mx
wrote:
Hi,
I just built gromacs 4.6.1 with intel compilers 13.0.1 on a machine with
Intel E5 2600 CPUs
After run the regression tests in single precision, I had two
was able to achieve
convergence.
I believe moving just 0.1 nm minimization will take care of correct
lengths. May be if its not the correct way; please suggest.
regards,
On Thu, May 2, 2013 at 12:50 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Wed, May 1, 2013 at 4:20 PM, gromacs
investigate. For something I'm
doing, I'd like to be sure the full T-coupling state is being exchanged,
and we may as well kill all the bugs at once.
Mark
XAvier.
On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri
On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote:
I saw that redmine report, which could be related but it seems to happen
only for runs done outside the domain and particle decompositions.
I'll fill up a red mine.
Anything I could do to help speeding the fix?
On Wed, May 1, 2013 at 2:50 AM, Sikandar Mashayak symasha...@gmail.comwrote:
Hi Justin
Thanks for explanation. But I am a bit confused because I am new to git.
When I check out release-4-6 branch, the source code should be the same as
the one in tarball from Gromacs website, right?
No. The
I mean simulate a single CO in a box. Then CO-with-vsite in a box. If you
can do that, then a bunch of problems are known to be solved. Leaping in
the deep end with a complex system means you don't know where the trouble
comes from when you have it.
Mark
On Wed, May 1, 2013 at 8:45 AM, 라지브간디
On Wed, May 1, 2013 at 5:40 PM, Sikandar Mashayak symasha...@gmail.comwrote:
Thanks Justin and Mark
I think I would checkout and create a branch from v4.6 tag.
You don't need a branch until you are going to develop something. And there
is no reason to make an install of an old point release
On Wed, May 1, 2013 at 3:16 PM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear
Mark,
As per you suggestion, I have simulated a single CO as well as
CO-with-vsite in a box.
A single CO runs without any problem, BUT the CO-with-vsite
gives an same error as before:
Steepest
Descents:
On Wed, May 1, 2013 at 2:32 PM, Reza Salari resa...@gmail.com wrote:
Hi Justin,
I actually did :) but it ended up being bigger than 50 kb so it needed
moderator approval to show up. I was hoping it would've been released by
now. I'll attach a the details below.
Any help/hint is highly
On Wed, May 1, 2013 at 4:20 PM, gromacs query gromacsqu...@gmail.comwrote:
Dear All,
I am using Charmm gui built membrane (120 x 2). But during minimization I
was getting error.
Potential Energy = 4.6809051e+19
Maximum force =inf on atom 4281
Norm of force =
verify this is
the case if you wish to do so, the original tarball is still available at
http://www.gromacs.org/Downloads under a new name.
Sorry for the confusion! Hopefully that is the last we see of autotools
with GROMACS :-)
Mark
On Fri, Apr 19, 2013 at 11:53 AM, Mark Abraham mark.j.abra
On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul jalem...@vt.edu wrote:
Please start a new thread if you're going to introduce a new topic. I
have changed the subject to something more relevant.
On 4/29/13 4:23 PM, lloyd riggs wrote:
*Dear All,*
*Doing a water/temp energy minimization
too late here for me to wrap my right-hand-rule for cross-products around
that one! :-)
Mark
On Tue, Apr 30, 2013 at 2:06 AM, Justin Lemkul jalem...@vt.edu wrote:
On 4/29/13 8:00 PM, Mark Abraham wrote:
On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul jalem...@vt.edu wrote:
Please start
Probably the part of the calculation done on the GPU is not rate limiting.
There's no point having four chefs to make one dish...
Look at the beginning and end of your .log files for diagnostic
information. If this is a single node, you should be using threadMPI, not
real MPI. Generally four CPU
On Sat, Apr 27, 2013 at 10:25 PM, Nathan Bullock bullocknathan...@gmail.com
wrote:
I created a text file called choices with the number corresponding to the
ions group. I then had the text file as an argument for the genion
function.
That cannot work. Read the link Justin provided.
Mark
AFAIK there is no magic number header. However, .trr files have frames of
constant size, so you can make a .tpr that will write a .trr file that will
include the longest period of your nst[xfv]out. Some Unix tool like dd (or
maybe hexdump) can probably tell you the size of that repeating unit.
On Fri, Apr 26, 2013 at 6:16 PM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear gmx,
I am having a trouble in setting the virtual site on CO molecule.
When I use V-site for CO, it end up with energy minimization error as
follows:
steepest Descents:
Tolerance (Fmax) = 1.0e+03
first.
Great. It may be that there were other issues in 4.5.3 that exacerbated any
REMD problem.
Mark
Tks.
On Apr 25, 2013, at 22:40, Mark Abraham mark.j.abra...@gmail.com wrote:
Thanks for the good report. There have been some known issues about the
timing of coupling stages
Likewise, I agreed with what Massimo said.
As an example, I recently did a fairly large set of REMD simulations of a
320-atom disordered peptide with rather more water and many fewer replicas
than you propose. I did so because I expected low barriers and large
maximum diameter (the latter from an
This works well until you use a system that permits job suspension. Then
-maxh gets double-crossed... :-)
Mark
On Apr 25, 2013 3:41 PM, Richard Broadbent
richard.broadben...@imperial.ac.uk wrote:
I generally build a tpr for the whole simulation then submit one job using
a command such as:
Thanks for the good report. There have been some known issues about the
timing of coupling stages with respect to various intervals between GROMACS
events for some algorithms. There are a lot of fixed problems in 4.5.7 that
are not specific to REMD, but I have a few lingering doubts about whether
me. Can you elaborate? Did they exchange?
On 25 Apr 2013 13:06, Mark Abraham mark.j.abra...@gmail.com wrote:
Likewise, I agreed with what Massimo said.
As an example, I recently did a fairly large set of REMD simulations of a
320-atom disordered peptide with rather more water and many fewer
X-C-CN-X is not present in amber03 in the GROMACS distribution. You seem to
be using some modified version. Please ask the person who modified it :-)
Mark
On Wed, Apr 24, 2013 at 4:26 PM, Elisa Frezza elisa.fre...@gmail.comwrote:
Dear All,
I am starting to use amber03 force field, but I
On Wed, Apr 24, 2013 at 8:14 AM, Venkat Reddy venkat...@gmail.com wrote:
Dear all,
I have got an analysis tool for analyzing membrane density from Dr.Luca
monticelli. I have followed the installation instructions as given.
1) First thing is to load GROMACS
$ *source
On Apr 22, 2013 4:47 AM, Ayesha Fatima ayeshafatima...@gmail.com wrote:
Dear All,
i am new to gromacs. I have already installed gromacs and using it for
some
basic simulation. i want to set up a parallel system since i have GPU and
CUDA installed Quad core CPU. I have been running amber on it
On Apr 20, 2013 11:13 PM, Susi Lehtola susi.leht...@alumni.helsinki.fi
wrote:
On Sat, 20 Apr 2013 22:15:09 +0200
Mark Abraham mark.j.abra...@gmail.com wrote:
True, I took no steps to make the old autoconf build system work. My
first 4.5.x tarball, sorry :-) The CMake build system definitely
for this new release.
I am very sorry, but ./configure doesn't work.
It returns bash: ./configure: No such file or directory
Luís
On 19 April 2013 10:53, Mark Abraham mark.j.abra...@gmail.com wrote:
Hi GROMACS users,
GROMACS 4.5.7 is officially released. It contains some bug fixes,
particularly
On Fri, Apr 19, 2013 at 3:30 AM, Fahimeh Baftizadeh
fahimeh.baftiza...@googlemail.com wrote:
Hello,
I have a 2 tpr files which are identical.
This is true only if gmxcheck agrees with you :-)
Then I am doing a single step MD
(I put n_step=0) simulation just to compute the total energy
Hi GROMACS users,
GROMACS 4.5.7 is officially released. It contains some bug fixes,
particularly for the md-vv integrator.
You can find the code, release notes, and installation instructions at the
links below.
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.7.tar.gz
On Apr 19, 2013 2:50 PM, Fahimeh Baftizadeh
fahimeh.baftiza...@googlemail.com wrote:
Hi thanks for your reply, and sorry to be late since I am living 9 hours
behind you :)
I tried but still I get different energies. I check tpr files, according
to
gmxcheck they are identical ...
But they
This is part of what state_prev.cpt is for - if only some of the new .cpt
files have made it to disk, you still have a full set of matching .cpt
files, but not with consistent names. Use gmxcheck to see the times.
Mark
On Fri, Apr 19, 2013 at 3:24 PM, andrea spitaleri
Identify the equations into which they are inserted. Apply scaling
parameters to change the units. Learn to check others' work before
investing months of effort ;-)
Mark
On Thu, Apr 18, 2013 at 5:39 PM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear gmx,
I m having a confusion of using the literature
Chapter 8 is your friend. Find a tool to feed data to g_analyze.
Mark
On Wed, Apr 17, 2013 at 4:23 PM, Steven Neumann s.neuman...@gmail.comwrote:
Dear Users,
Could you advise me please how to calculate vector C-N autocorrelation
function in my protein along the simulation time?
Steven
No idea. Configuring your MPI system is not really on topic for the GROMACS
mailing list. I suggest you read your OpenMPI documentation.
Mark
On Thu, Apr 18, 2013 at 2:58 PM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear Gmx,
Is there anyway I can run simulation using mpirun command via rsh? I am
that, since this information is usually took from .trr or
.xtc, it cannot
be extracted from a .dcd, but it could be more useful using as x the frame
number.
This could, at least, permitting to visualize the plot with xmgrace without
postprocessing
the .xvg
Francesco
2013/4/16 Mark Abraham
On Apr 16, 2013 6:28 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I obtained a POPC lipids from CHARMM-GUI and I found the initial 12
line are following:
following atom name order:
ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29
MEMB
ATOM 6316 C12 POPC 22
That's best. GROMACS will take care of a _d suffix for double precision for
you.
Mark
On Mon, Apr 15, 2013 at 5:39 PM, Mike Hanby mha...@uab.edu wrote:
Howdy,
What's the proper procedure for building both single and double precision
and installing them to the same directory?
For example,
On Apr 15, 2013 6:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/15/13 12:23 PM, Steven Neumann wrote:
Dear Gmx Users,
I obtained dcd trajectory from simulation in another software. I wish to
merge many trajectories using trjcat with a proper timestep. Is that
option
possible using
I've no idea what the real limitation in InflateGRO might be, but if it is
based on the [moleculetype], then a combined protein+ligand [moleculetype]
might be effectlve.
Mark
On Sat, Apr 13, 2013 at 2:38 PM, Justin Lemkul jalem...@vt.edu wrote:
On Sat, Apr 13, 2013 at 4:57 AM, swati rana
, IBM_QPX
-- Configuring incomplete, errors occurred!
-
Could you give me some advise? Thank you very much!
Best,
Yukun
2013/4/12 Mark Abraham mark.j.abra...@gmail.com
On Thu, Apr 11, 2013 at 5:41 PM, Yorquant Wang wangy...@gmail.com
0.0 -2.61082
0.0 0.0
HP42 CBD CGD O2D30.65270 1.95811 0.0 -2.61082
0.0 0.0
I believe so.
Do I need to remove these definitions from the ffbonded.itp files then?
Unused entries do no harm.
Mark
- Laura
On 04/11/2013 05:43 PM, Mark Abraham
That looks really strange. CMake claims to detect CUDA but the right
variables are not set.
1) Can you reproduce this in a clean build directory?
2) If so, what CUDA is present?
Mark
On Thu, Apr 11, 2013 at 2:57 PM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear gmx,
I have installed mpich for MPI
On Fri, Apr 12, 2013 at 11:28 AM, Thomas Evangelidis teva...@gmail.comwrote:
On 12 April 2013 07:51, anu chandra anu80...@gmail.com wrote:
Hi David,
Thanks for the reply. I have not tried yet. Since I didn’t find query
about
the dihedral PCA in the mail list, I thought of confirm about
Hi Natalia,
I am not aware whether the QM/MM implementation in GROMACS works in 4.6,
nor with which Gaussian version was intended to work in the past. Perhaps
Gerrit Groenhof or someone on gmx-users can update us here?
I'm not sure what diff file you are seeking, either. Can you elaborate
On Fri, Apr 12, 2013 at 5:53 PM, Hua Lu h...@greenwich.ac.uk wrote:
Hi!
I got the following error message while compiling gromacs using a complete
installation of Cygwin on 64bit windows 7. Any idea what the problem is?
Yes, you can't read those files. We can't know why. You wrote them as a
On Thu, Apr 11, 2013 at 8:14 AM, 陈照云 chenzhaoyu...@gmail.com wrote:
I have tested gromacs-4.6.1 with k20. But when I run the mdrun, I met some
problems.
1.Configure options are -DGMX_MPI=ON ,-DGMX_DOUBLE=ON -DGMX_GPU=OFF .
But if I run parallely with mpirun, it would get wrong.
Note: file
thing though: The average energy (mu) returned by the web server for
each temperature is 7-8 times more than the actual energy returned after
REMD was over.
Is there something we are missing here?
Thanks.
On Tue, Apr 9, 2013 at 6:42 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Tue, Apr
On Thu, Apr 11, 2013 at 7:07 AM, 申昊 shen...@mail.bnu.edu.cn wrote:
Hello,
I wanna ask some questions about load imbalance.
1 Here are the messages resulted from grompp -f md.mdp -p topol.top
-c npt.gro -o md.tpr
NOTE 1 [file md.mdp]:
The optimal PME mesh load for
On Thu, Apr 11, 2013 at 11:05 AM, 陈照云 chenzhaoyu...@gmail.com wrote:
How to run combinedMPI/OPENMP parallelization with 2 or 4 Openmp threads
per MPI process?
GMX_OPENMP is on by default, and works automatically (where it can). See
It probably shouldn't do anything. However, at least the documentation
should be better here. Does it work? Does it differ from
vdw-type= Switch
vdw-modifier=None?
Mark
On Thu, Apr 11, 2013 at 2:13 PM, Chrisostomos Batistakis
tomyvanba...@gmail.com wrote:
Dear all
I have started
On Thu, Apr 11, 2013 at 5:41 PM, Yorquant Wang wangy...@gmail.com wrote:
Hello:
I have installed GMX4.6.1 and GMX4.5.5 on the same cluster. There are
2 Xoen E5 2630CPU in one node on this cluster. I tested the performance of
those two versions of GMX, found GMX4.6.1 only had 0.62
Do a short simulation that will be representative. Measure. Use
multiplication.
Mark
On Thu, Apr 11, 2013 at 8:30 PM, Sikandar Mashayak symasha...@gmail.comwrote:
Hi
I would like to determine an estimate of hard disk space required to
perform a typical MD simulation using gromacs. To do
Like I said yesterday when you posted this question from a different email
account...
Your system is blowing up because it's unstable. Where did you get this
protocol? I suggest starting by reproducing something similar that has been
published :-)
On Thu, Apr 11, 2013 at 3:11 PM, aviv naftaly
Look in the literature...
On Thu, Apr 11, 2013 at 2:12 PM, James Starlight jmsstarli...@gmail.comwrote:
During the past few days I've tried to make parametrization of any
heme-containing cythochromes and always failed with the huge errors about
missing parameters. Could someone provide me
Type 9 was added at some point to GROMACS to make coping with AMBER and
CHARMM easier. So you should just change your #defines from 3 to 9. See
table in chapter 5. Or you could just leave your solution in the same form
as you did for the 4.0.x GROMACS.
Mark
On Thu, Apr 11, 2013 at 10:36 PM,
. Only the
latter needs the atom types (because that's how the lookup works). The
old-style #defines cannot work in ffbonded.itp, because they assume the
context of the .rtp, where the atoms are already identified.
Mark
On 04/11/2013 04:51 PM, Mark Abraham wrote:
Type 9 was added at some
On Wed, Apr 10, 2013 at 8:49 AM, Anna Marabotti amarabo...@unisa.it wrote:
Dear gmx-users, dear Mark,
the soap-opera is going on... and I am so sorry to bother you again and
again (but I hope that this will be of help for future people that will
have the same problem...).
Summary of the
On Wed, Apr 10, 2013 at 5:25 PM, Anna Marabotti amarabo...@unisa.it wrote:
Dear Mark,
I am really exhausted about this story. I read your message below, and if
I understand correctly, nothing is apparently wrong in what I'm doing,
however things are not going at all.
Following your
On Wed, Apr 10, 2013 at 3:49 PM, Liron Cohen liron.co...@weizmann.ac.ilwrote:
hi,
i am using gromacs 4.5 and i am trying to run an energy minimization and
then temperature equilibration for a system of two charged plates plates
solvented in water.
the plates are made of fake atoms which has
in my limited
knowledge of gromacs that I have gained in the past couple of days.
Please advice
On Tue, Apr 9, 2013 at 6:39 PM, Mark Abraham mark.j.abra...@gmail.comwrote:
On Tue, Apr 9, 2013 at 8:33 AM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:
So there is a problem with your trajectory
I was using an old version. Now I used 4.5.5, it still gives me the
same
blank output file.
Kindly suggest how to go about solving this
Thanks
On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham
mark.j.abra...@gmail.com
wrote:
On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy venkat
On Tue, Apr 9, 2013 at 10:44 AM, Nikunj Maheshwari
nixcrazyfor...@gmail.com wrote:
Thats true with our case as well. The spacing was very small, and we got
almost 70 replicas for our protein between 280-410K.
That's why, we are thinking of any alternate way of getting the spacing,
and started
On Tue, Apr 9, 2013 at 12:26 PM, Anna Marabotti amarabo...@unisa.it wrote:
Dear gmx-users, dear Mark,
I still have problems with my parametrization, and I wrote a message
describing in details the problems, but it appears to be too large and it is
being held on hold (see below). How can I send
On Tue, Apr 9, 2013 at 8:29 AM, Shine A shin...@iisertvm.ac.in wrote:
Respected sir,
I successfully completed REMD simulation. Now I am
struggling with analysis part. Here how I select the global minimum from
replica? Can you give some suggestions about the analysis
On Tue, Apr 9, 2013 at 9:59 AM, James Starlight jmsstarli...@gmail.com wrote:
By the way during simulation of the membrane-protein systems in the
Amber99sb ff (with berger lipids) I've noticed decreased of my system in
the Z-direction ( I've observed the same also during simulation of such
On Apr 10, 2013 3:34 AM, Benjamin Bobay bgbo...@ncsu.edu wrote:
Szilárd -
First, many thanks for the reply.
Second, I am glad that I am not crazy.
Ok so based on your suggestions, I think I know what the problem is/was.
There was a sander process running on 1 of the CPUs. Clearly GROMACS
Indeed. New players will benefit from
http://www.hpcwire.com/hpcwire/2011-12-13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus.html:-)
Mark
On Apr 9, 2013 5:59 PM, Justin Lemkul jalem...@vt.edu wrote:
On Tue, Apr 9, 2013 at 11:38 AM, Andrew DeYoung adeyo...@andrew.cmu.edu
You might use freeze groups or position restraints depending what you want.
See manual.
Mark
On Apr 8, 2013 2:58 AM, Juan Antonio Raygoza Garay raygo...@psu.edu
wrote:
Hi, is it possible to instruct gromacs to only perform the dynamics on
half of the system or protein while ignoring the rest?
Yes, there's no way to cheat on the explicit electrostatics to reduce cost,
except implicit solvation. The kind of approach used in QM/MM is not useful
for MM/MM! The rate-limiting part is still there.
Mark
On Apr 8, 2013 12:42 PM, Justin Lemkul jalem...@vt.edu wrote:
On Mon, Apr 8, 2013 at
On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com
wrote:
Dear all,
Due to cluster wall-time limitations, I was forced to restart two REMD
simulations. It ran absolutely fine until hitting the wall-time. To
restart
I used the following command:
mpirun -np 64
These are almost irrelevant for performance. What are you actually
simulating on what?
Mark
On Apr 7, 2013 2:12 AM, 陈照云 chenzhaoyu...@gmail.com wrote:
Hi!
I have 6 nodes. Each node has two CPUs,12 cores totally.
How should I set the options like -rdd,-rcon,-dds,-gcom to improve the
, Mark Abraham mark.j.abra...@gmail.com
wrote:
On Apr 8, 2013 8:53 AM, João Henriques joao.henriques.32...@gmail.com
wrote:
Dear all,
Due to cluster wall-time limitations, I was forced to restart two REMD
simulations. It ran absolutely fine until hitting the wall-time
On Sat, Apr 6, 2013 at 8:25 AM, Chandan Choudhury iitd...@gmail.com wrote:
You need to re submit the jobs, with decreased time.
And next time check with the manual and consider your needs before making
arbitrary choices :-)
Mark
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat,
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