I often use 4 fs with all-bonds and virtual sites, especially if lacking
sampling is a greater source of error than the kinetic energy being slightly
off.
Erik
On 15 Aug 2013, at 20:58, Michael Shirts mrshi...@gmail.com wrote:
I don't go beyond 2 fs with either all- bonds or h-bonds. Things
* Time
* Ac(hbond) with correction for the fact that a finite system is being
simulated.
* Ac(hbond) without correction
* Cross correlation between hbonds and contacts (see the papers by
LuzarChandler and van der Spoel that are mentioned in the stdout from g_hbond)
* Derivative of second column.
It's just the xvv file. g_wham uses the letter 'z' to denote the reaction
coordinate.
Erik
On 2 Jul 2013, at 11:32, battis...@libero.it wrote:
Dear users and experts
I'm doing an umbrella-samplig calculation to obtain the PMF when two
structure (A and B) are at various X
Hi,
Yes, the forward and backward rate constants are for hydrogen-bond breaking and
reforming. You seem to have too poor statistics to draw conclusions about the
backward rate, however. You probably need to simulate longer.
Erik
On 15 Jun 2013, at 00:38, learnmd joinforfun8...@gmail.com
…or the hydrogen-bond kinetics of your system may not fit the Luzar-Chandler
model for whatever reason.
Erik
On 17 Jun 2013, at 13:22, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
Yes, the forward and backward rate constants are for hydrogen-bond breaking
and reforming. You seem to have
Hi,
Search the mailing list. This problem and its solution has been repeatedly
discussed.
Erik
On 12 Jun 2013, at 10:31, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Dear all,
I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
I am trying to use it for do_dssp
On 12 Jun 2013, at 11:17, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Yes I did searched. But for most people, there were issues regarding the
path or wrong DSSP.
DSSP runs for me, but do_dssp does not.
On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi
I checked. do_dssp has no -ver option.
I also found out this link
https://gerrit.gromacs.org/#/c/687/
but dont know how to install/use it.
Or maybe I can install DsspOld and see?
On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Search again. The syntax
HI,
What version of gromacs is this? DSSP changed its syntax a while back and we
had to adjust do_dssp accordingly. You may have a mismatch between gromacs and
dssp versions.
Erik
On 7 Jun 2013, at 08:42, Nur Syafiqah Abdul Ghani pqah...@gmail.com wrote:
Hi All,
I already done the MD
which is available through the dssp webpage.
Erik
On 7 Jun 2013, at 10:20, shika pqah...@gmail.com wrote:
Hi Eric,
I'm using gromacs 4.5.5.
Is it the version is different for dssp?
Thanks
On Fri, Jun 7, 2013 at 3:41 AM, Erik Marklund [via GROMACS]
ml-node+s5086n5008885...@n6.nabble.com
Hi James,
Not related to the integration stability as such, but since the vsites affect
the hydrogens by definition perhaps g_hbond can reveal systematic differences
between simulations with and without vsites. I believe Feenstra et al did this
in the paper describing vsites in the first
How about running with -noappend?
On 1 Jun 2013, at 13:59, vidhya sankar scvsankar_...@yahoo.com wrote:
Dear Justin Thank you for your previuos reply
I am
using gromacs 4.6 AMD 8 core processor
When I run restart My run
gcc is probably still your old version. The new one would probably be called
gcc-4.7 or similar.
Erik
On 30 May 2013, at 15:15, vidhya sankar scvsankar_...@yahoo.com wrote:
Dear Justin and other gromacs users ,
Thank you
Hi,
I have achieved good energy conservation in NVE simulations. This was single
proteins in the gas phase, using infinite cut-offs, constraints applied to
hydrogens, 0.5 fs or 1.0 fs time steps, double precision and virtual sites if
I'm not mistaken. We had problems with energy conservation
Hi,
Just to clarify: The third column are the number of acceptor-donor pairs that
fulfil the distance criterion but not the angle criterion.
Erik
On 24 May 2013, at 09:06, CHEN Pan evan.pan.c...@gmail.com wrote:
Hi Maggin,
The middle column is the total number of hydrogen bonds in your
Hi,
See below
On 24 May 2013, at 11:45, CHEN Pan evan.pan.c...@gmail.com wrote:
Dear Gromacs users,
I am confused about the g_hbond tools.
1) When I use -dist to get the distribution of hydrogen bonding distance,
I found that the summation of the population is always 200 (the y-column
, which I
should get 512 hydrogen bonds. And the output hbnum.xvg does show 512
hydrogen bonds, which is correct. But the hbdist.xvg file still shows
that the summation of population is 200.
2013/5/24 Erik Marklund er...@xray.bmc.uu.se
Hi,
See below
On 24 May 2013, at 11:45, CHEN Pan
bonding energy, but I haven't see any flag command
could give a output of hydrogen bonding energy file. Is it still under
development?
2013/5/24 Erik Marklund er...@xray.bmc.uu.se
Hm. That is peculiar. The source code has the answer of course. I can have
a look next week to see why
g_hbond and g_hbond -contact
Erik
On 22 May 2013, at 05:37, Vishal Kumar Jaiswal vishal3...@gmail.com wrote:
Hello gromacs users
I performed a 1 ns simulation of N-isopropylamide in water. Now i wish to
calculate the average no of water molecules(averaged over entire
trajectory) within a
Hi,
For particles that diffuse more than half a box length between frames will
appear as if they haven't moved much, assuming you have periodic boundary
conditions.
Erik
On 22 May 2013, at 11:41, Anna Akinshina anna.akinsh...@manchester.ac.uk
wrote:
Dear Gromacs Users,
I have a question
Hi,
To get useful help with this issue you need to provide a more informative
description of what when wrong, i.e. what gromacs tool was invoked and what
input was used.
Erik
On 20 May 2013, at 10:59, Pruthvi Bejugam pruthvi.n...@gmail.com wrote:
Hi all,
I want to perform
HI,
s0, s1,… is (xm)grace codes that refer to the different datasets in the file.
Gromacs prints the datasets as different columns. I suggest opening the file
with xmgrace -nxy yourxvgfile.xvg. As for the -life option, the results are
based on a too wimple kinetic model for most applications.
Hi,
Have a look at the following article. It describes a non-standard box type that
seems ideal for your application. I don't know what is the latest gromacs
version where it is implemented, however.
Author = {Wassenaar, TA and Mark, AE},
Title = {{The effect of box shape on the dynamic
/home/dssp seems like a strange path. Are you sure you set DSSP correctly?
Erik
On 8 May 2013, at 15:19, Sainitin Donakonda saigr...@gmail.com wrote:
Hello,
I am trying to secondary structure analysis using DSSP in gromacs so i
followed this procedure
First I downloaded dssp
wget
I really don't think thats possible at the moment. All interactions in Reax, if
I recall correctly, are dependent on bond order, which is not an implemented
concept in gromacs.
Erik
On 6 May 2013, at 12:51, Sathish Kumar sathishk...@gmail.com wrote:
hai
i would like to use Reax
There's no general answer to that. Proton conductivity measurements, for
instance, will be horribly wrong without dynamic protonation. Much (but not
all) structural biology, however, will be largely unaffected.
Erik
On 3 May 2013, at 04:30, shahid nayeem msnay...@gmail.com wrote:
Dear all
If I recall correctly it uses the seed provided in the mdp file. If no seed is
provided it uses the process id for seeding. The manual explains the details.
Erik
On 3 May 2013, at 08:00, Preeti Choudhary preetichoudhary18111...@gmail.com
wrote:
hey this is regarding random seed used in
, Erik Marklund er...@xray.bmc.uu.se wrote:
There's no general answer to that. Proton conductivity measurements, for
instance, will be horribly wrong without dynamic protonation. Much (but not
all) structural biology, however, will be largely unaffected.
Erik
On 3 May 2013, at 04:30, shahid
of
protonation/deprotonation equilibria is accounted for while my question
relates to the typical constant protonation MD where each titratable group
remains in one protonation state throughout the simulation. Please educate
me
Shahid
On Fri, May 3, 2013 at 6:22 PM, Erik Marklund er
You seem to be using a 2 fs time step. It's difficult to achieve stable
integration using 2 fs time steps in vacuum. Please provide more information
about your simulation parameters.
Erik
On 2 May 2013, at 14:40, Souilem Safa safasouil...@gmail.com wrote:
Dear Gromacs users ,
I did the
Average coordinates are problematic and not generally representative. Consider
for instance the average coordinates of a methyl group connected to X. The
rotation around the C-X bond causes the average positions of the hydrogens to
line up. Consider using g_cluster to find representative
Hi,
Could you please clarify if the hbond existed in frames for which g_sdangle
reported a ADH-angle above 30 deg?
Also, bear in mind that the -merge flag is on by default, so another hydrogen
may bridge the donor-acceptor gap.
Erik
On 24 Apr 2013, at 21:09, kim2811 kmani...@iastate.edu
The gromacs web page links to this server for REMD temperature generation:
http://folding.bmc.uu.se/remd/
On 9 Apr 2013, at 08:34, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Hi. Glad to know that your REMD was successful. We are trying to do the
same, but are stuck in between.
Can you
I've tried one with 666 aa, but with no publishable results.
On 9 Apr 2013, at 09:47, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote:
Dear all...
Does anyone has any idea what is the maximum protein size for which a
successful REMD run has taken place?
We have went through lots of
you get the final temperature spacing for the run? Did you get the
fitted values using polynomial fit?
Was the run completed?
On Tue, Apr 9, 2013 at 1:27 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
I've tried one with 666 aa, but with no publishable results.
On 9 Apr 2013, at 09:47
There's a known oscillation in the ACF that occurs at ~100 fs or so. Is that
what you see?
Erik
On 9 Apr 2013, at 18:02, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
ndhu...@andrew.cmu.eduwrote:
Hello,
I am calculating the hydrogen bond
It is, and I think there was in fact some experimental/private branch that
dabbled with this. It hasn't gone into the official releases yet and there is
no guarantee that it will.
Erik
On 4 Apr 2013, at 14:10, nahren manuel meetnah...@yahoo.com wrote:
Sorry to bother you all once again. As
I always do. There's nothing particular about umbrella sampling in this respect.
On 4 Apr 2013, at 17:33, raghav singh raghavbioi...@gmail.com wrote:
Hello Fellow Users,
I have a question regarding US simulation.
I am interested to know that can I treat hydrogens as virtual sites in US
Yes.
On 3 Apr 2013, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am calculating the hydrogen bond life time for my system.
Do program consider the hydrogen bond criteria for calculation of
autocorrelation function?
Nilesh
--
gmx-users mailing list
On 2 Apr 2013, at 13:30, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 7:13 AM, rama david wrote:
Dear friends,
I am naive to the Replica exchange Molecular dynamics ( REMD).
I have plan to use REMD for temp. 310-320 K to my system.
I thoroughly search the Mailing-list
Hi,
I suggest contacting people in Johan Åqvist's lab. I'm sure they know exactly
what pitfalls there may be with regards to the choice of LIE parameters and
what has been done for different types of molecules.
Erik
On 26 Mar 2013, at 02:42, Vishwambhar Bhandare vishway...@gmail.com wrote:
+MS +SS)
hydrogen bond.
Is there any other solution?
Thank you
Kavya
On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M hmkv...@gmail.com
wrote:
Dear Sir,
Sure I will try with 4.6. presently I am not able to download it.
Thank you
kavya
On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund
er
, 2013 at 4:04 PM, Erik Marklund
er...@xray.bmc.uu.se
wrote:
There were a handful of bugfixes to g_hbond over the last year.
Could
you
try 4.6 or a smoking hot 4.5.5? I recognize this discrepancy form
before.
Erik
On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:
Dear Sir,
This is 4.5.3
On Mar 19, 2013, at 11:45 AM, Justin Lemkul wrote:
On 3/19/13 5:44 AM, 라지브간디 wrote:
Anyone tell me how do I freeze the particular residues in NPT-NVT
equillibrium steps ? I want them in same conformation as pdb for
further production run ? Thanks in advance
Use freezegrps or strong
Hi,
I believe there is no force output for constraint pulling. Try umbrella.
Erik
On Mar 18, 2013, at 3:28 PM, raghav singh wrote:
Hello Fellow Users,
I am trying to pull a DNA molecule. I have fixed one end and trying
to pull
the other one using this .mdp file.. force output is all
Hi,
You also need to consider the ensemble you want to investigate. If you
simulate under constant energy you need a shorter timestep than you
would have in solution and probably double precision. In the articles
I list below we used a timestep of 0.5 fs and 1 fs, respectively, and
Restraints allow, by definition, for slight deviations.
Erik
On Mar 14, 2013, at 12:51 PM, Shima Arasteh wrote:
Dear gmx users,
I want to use restraints on backbone of my protein to keep its
secondary structure during minimization and equilibration steps. To
do so, I generated
Do you really mean compile time? If so, issue make -j X (where x is
the number of jobs used for building).
If you mean runtime then the easiest thing is to split your trajectory
in parts and run the processes in parallel, then patch the results
together. That's if the calculations can be
Gromacs currently use OpenMP and/or MPI with it's own wrappers for
parallel computation. There is a general framework being developed for
parallelizing analysis tools, but I don't know the specifics and I
beleive it's not ready for use yet.
Is that helping you?
Erik
On Mar 14, 2013, at
On Mar 7, 2013, at 2:59 AM, Justin Lemkul wrote:
On 3/6/13 8:57 PM, Vishwambhar Bhandare wrote:
dear gromacs user,
how i can do binding free energy calculation for RNA duplex in
gromacs?
any tutorial for the same??
Free energy calculations involving interactions between
macromolecules
From the manual it seems that oscillating electric fields are not yet
implemented, which surprised me. I've seen colleagues use such in
gromacs, but that may have been in-house modifications. Should be
fairly simple to implement though.
Erik
On Mar 4, 2013, at 11:30 PM, raquick wrote:
To clarify: the -hbn output is not very indicative of how many
contacts there were since some of them could be present in one frame
but absent in 99. The -num option, however, provides the number of
contacts over time, and its time average probably tells you much more
in this case.
!
Thank you
kavya
On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se
wrote:
To clarify: the -hbn output is not very indicative of how many
contacts
there were since some of them could be present in one frame but
absent in
99. The -num option, however, provides the number
As Justin implied, -merge could potentially make a factor of 2. Try
g_hbond -nomerge.
Erik
On Mar 4, 2013, at 4:02 PM, bipin singh wrote:
Thanks for the reply.
The difference is almost double, through g_hbond the average number of
contacts are 1821 and through g_mindist it is 3643. The
decided to try an older version before going into the trouble
itself...
Kind of coward, I know, but the troubles with that version are already
reported so that I thought things would be easier :)
Thank-you a lot for your comments
2013/3/1 Erik Marklund er...@xray.bmc.uu.se
Interesting
)
by this sed will remove 35SOL not 135SOL.
regards,
On Fri, Mar 1, 2013 at 5:27 PM, Erik Marklund er...@xray.bmc.uu.se
wrote:
Hi,
Then the problem lies in automating what molecules are to be removed,
right? Try g_select or look into trjorder.
Erik
On Mar 1, 2013, at 2:45 PM, gromacs
With -ver, just like it says. do_dssp -h explains how. What dssp
version do you have?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD
The ndx format is really simple. You can easily script your way to a
new index group as long as the selection of atoms can be automated.
Furthermore, the gro format is also simple, so you can filter out the
unwanted residues there instead of using an index file.
Erik
On Mar 1, 2013, at
What happens if you execute the command (/usr/local/bin/dssp/ -i
ddQ3PqtX -o ddR1HavD) in your terminal?
Erik
On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error
you got:
dssp cmd='/usr/local/bin/dssp/ -i
.
thanks,
This gave me del.gro having residues mentioned in index file. But I
want
del.gro file without the residues mentioned in index file.
On Fri, Mar 1, 2013 at 2:48 PM, Erik Marklund er...@xray.bmc.uu.se
wrote:
The ndx format is really simple. You can easily script your way to
a new
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of
using an
index file.
There are thousands of water to be removed so simple commands like
sed
exhausts when I run
, 2013 at 3:09 PM, Erik Marklund er...@xray.bmc.uu.se
wrote:
On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
Dear Erik,
so you can filter out the unwanted residues there instead of
using an
index file.
There are thousands of water
I get I plot very small,
where one barely can see the colour code and the legend is sooo big.
Does
anyone know how to change that?
2013/3/1 Erik Marklund er...@xray.bmc.uu.se
What happens if you execute the command (/usr/local/bin/dssp/ -i
ddQ3PqtX
-o ddR1HavD) in your terminal?
Erik
at 3:38 PM, Erik Marklund
er...@xray.bmc.uu.sewrote:
Perhaps g_hbond -contact will do what you want.
Erik
On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
Dear users,
How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr writes
Perhaps g_hbond -contact will do what you want.
Erik
On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
Dear users,
How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr writes
with the option -sep.
I tried using g_mdmat but it
On Feb 14, 2013, at 2:01 PM, Justin Lemkul wrote:
On 2/13/13 5:23 PM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu
wrote:
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul jalem...@vt.edu
wrote:
On
Hi,
I have used MacroMolecule Builder for similar things.
Erik
On Feb 13, 2013, at 4:41 AM, zugunder wrote:
Hi,
I am sorry if this topic is not relevant for GROMACS forum, but I hope
someone has faced the same problem before and could give me some
advice...
I need to simulate a
It shouldn't generate output. It will make your system find your
gromacs installation, however. Try e.g. which mdrun.
Erik
On Feb 13, 2013, at 5:06 AM, David Sáez wrote:
Thanks for your answer Justin. I followed your advice:
When I type
*$ source /usr/local/gromacs/bin/GMXRC*
*$*
Nothing
Try virtual sites constructions.
On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote:
Dear All,
I need to define interaction sites on the center of C-H bonds instead
of nuclei of each atom. The main reason was that non-bonding
parameters (sigma and epsilon) have been parametrized in these
Hi,
Perhaps a side point: Temperature and pressure can not be seen as
constraints to the system at any given instant in the sense that e.g.
the instantaneous kinetic energy perfectly match the temperature at
every time step just because you have a thermostat. Time and ensemble
averages
I've never seen good parameters for nucleic acids. There might be
such, but none that ship with gromacs as far as I know.
Erik
On Feb 7, 2013, at 4:25 AM, 김현식 wrote:
Dear experts,
Hello!
Is it possible to run RNA md with GBSA?
Thank you.
bestKim.
On Feb 5, 2013, at 8:22 AM, bipin singh wrote:
Hello All,
Please let me know whether is it possible to manually assign the
velocity
for each atom in the simulation instead of generating through gen_vel
option.
If the preceision of a gro-file is sufficient you can use such for
manually
Hi,
If you don't care about the exact distances, but rather the time the
groups spend within a certain distance, g_hbond -contact can be useful.
Best,
Erik
On Feb 3, 2013, at 6:36 PM, James Starlight wrote:
Justin,
1 )for example I want to select in index file only all asp, glu and
his
HI,
It should read trjconv. And all analysis tools have the -b and -e
flags for excluding the start or the end of a trajectory.
Erik
On Feb 4, 2013, at 7:00 AM, Emanuel Birru wrote:
Use trajconv
http://manual.gromacs.org/online/trjconv.html
-Original Message-
From:
Short answer is to inspect your complex with VMD or Pymol (or some
other viewer). Pymol takes pdb input, so unless your structure is
contained in a pdb file you must convert it with e.g. trjconv first.
If you want a single frame you need to extract one form your
trajectory, or, if the
On Jan 25, 2013, at 5:53 AM, Shima Arasteh wrote:
Thanks for your reply.
I want to chose one of the 5 conformers from a NMR PDB. As I studied
in literature, the average structure could be selected regarding
RMSD values and the go on with selected one to simulate in in water,
lipid
, Erik Marklund
er...@xray.bmc.uu.se wrote:
Hi. What version was this? Have you tried with -nomerge?
Erik
On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
Dear users,
While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds
Hi. What version was this? Have you tried with -nomerge?
Erik
On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
Dear users,
While calculating hydrogen bonds for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds.
g_traj -nox -noy if I recall correctly.
On Jan 21, 2013, at 4:10 PM, Albert wrote:
hello:
I would like to make statics for an atom along Z-axis. I am just
wondering how can I to do this in Gromacs?
thank you very much
best
Albert
--
gmx-users mailing listgmx-users@gromacs.org
Hi,
If you're simulating in the gas-phase, how come you want implicit
solvent?
Erik
On Jan 11, 2013, at 5:07 AM, Sanku M wrote:
Hi,
I am trying to do implicit solvent simulation for a protein in gas-
phase. I have a few questions :
1) should I use sd integrator?
2) should I also use
the
www interface or send it to gmx-users-requ...@gromacs.org.
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phone:+46 18 471 6688fax: +46 18 511 755
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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the outcome of
starting several trajectories from the same equilibrated frame as
continuation runs, i.e., using its velocities? Could they be considered
independent and used to extract that valuable statistics mentioned in a
previous posting?
Felipe
On 11/22/2012 10:04 AM, Erik Marklund
10:04 AM, Erik Marklund wrote:
Stochastic and chaotic are not identical. Chaotic means that differences
in the initial state will grow exponentially over time.
Erik
22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD:
Won't this same stochastic nature of MD provide for different
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
is to write a simple script that parses out the columns you
want.
-Justin
I don't see the point though. Except for checking implementation of the pull
code.
---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Erik Marklund [er...@xray.bmc.uu.se]
Sent: 15 November 2012 13:37
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Dihedral form
You could shift the reference angle
post? Read http://www.gromacs.org/Support/Mailing_Lists
---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
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gmx-users mailing list
/Support/Mailing_Lists
---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio
,
and in the other case the distance between two proteins is less than the cut
off value,
Bests
-Zahra
From: Erik Marklund er...@xray.bmc.uu.se
To: Zahra M s_zahra_mous...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Tuesday, November 13, 2012 2:08 PM
Subject
/Support/Mailing_Lists
---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab
---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
--
gmx
, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms
on 192 cores at ~45 ns a day. with half the number of processors I get ~27
ns a day. It will of course depend on the hardware, particular algorithms,
run parameters
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