First of all, sorry for the late answer.
More generally it is said the the rupture force depends logarithmically
on the loading rate (velocity times spring constant). - So the
rup.force should also depend logarithmically on the spring constant (in
the simple bell modell).
Think the reason,
Think your .mdp-file looks reasonable.
If you are totaly unsure you could determine the PMF of two water
molecules. As a reference one can use the radial distribution function
g(r) and calculate the PMF as
V_pmf(r) = -kT LN(g(r))
One side note:
Since the force constant you are using is
Hi,
the following:
trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep
should work.
-dt 250 ; write output every 250 ps
-sep ; to write each frame (but the output frequency gets overwritten by
'-dt 250')
the additional use of '-dump x' might be the problem, since with '-dump
x' GMX writes
But you need each of these lines for both cases (SMD and US). Probably
one could skip two lines and use the default values, but it's better to
set them manually. See below for comments (comments are under the
related entry):
Thanks for your reply. But when I don't understand why these extra
In GROMACS groups are called via the *.ndx file (default: index.ndx)
Be aware that 'pull_dim' determines in which diretions (x,y,z) the
umbrella potential acts. So use N N Y , if you want that the ion can
move freely (onsidering the pull) in the xy-plane and Y Y Y if you want
to also restrit
Generally:
Using a higher force constant and / or pulling velocity drives the
system faster out of equilibrium, which results in higher rupture forces.
Varying the force constant has two effects. The softer the potential is,
the larger are the fluctuations in the coordinates but the lower are
I see the same problem as Justin.
The real problem lies here:
mdrun -nt 4 -v -s 10step.tpr -c nonlinear.gro -e nonlinear.edr -x
nonlinear.xtc -o nonlinear.trr -g nonlinear.log -cpi nonlinear.cpt -cpo
nonlinear.cpt -rdd 2.5
Due to the '-cpi nonlinear.cpt' mdrun thinks the the time now the
If you use periodic boundary conditions, there is no need that the
protein stays at one side of the box.
For the pulling simulation: Read the chapters 6.4 (explains the
pull-code) and 7.3.21 (explains the mdp-paramters).
Additional information you an also get from Justin Tutorial for Umbrella
Sorry, my writing was not really excat.
If you use a reference group, the force / potential acting on the pulled
group is always relative to the reference group.
If you use 'pull_geometry = distance' the origin potential is always in
the distance 'pull_init1' along the vector from the reference
Look also into the manual. But the tutorial is a nice place to start.
For further comments see below:
Dear Lloyd,
I have read that but my system is different
regards,
On Thu, May 30, 2013 at 8:28 PM, lloyd riggslloyd.ri...@gmx.ch wrote:
Dear Jiom,
Look at justines tutorial, there's
For comments to your questions see below.
More general: (somewhat longer than i wanted. Hope you find some answers
here)
Imagine two interacting particles A and B which are alinged to the
x-axis. We take A as the reference group, B as pulled group and put the
origin of the umbrella
The three steps (EM, NVT and NPT) are to equilibrate the system. How
much time these steps need depends on the system. But i would assume a
ouple of nanosecounds are sufficient for most systems. You could look
into the literature, how long other people equilibrate systems which are
similar to
Dear all,
if one performs a parallel calculation on a single node / computer with
more than 1 core, is there a speed difference between MPI and Threads?
Problem is for gromacs 4.6.1 i'm facing problems to link it to OpenMpi.
A serial version (without threads) worked, so i think i should be
Hi,
it seems that you've only coupled your protein to the thermostat, but
not the solvent, hence the error message.
Generally one would couple both domains of the protein to one thermostat
and the solvent (inluding ions) to another thermostat.
Side note: If you want to use the WHAM method for
Hi,
the manual mentions that with the option '-surf' no normalization is
done. So it's normal the RDF will inrease with larger distances, since
the further you'll go away from the protein, the bigger the spherical
shell is (from which the RDF for distance r is calculated) and the more
water
If you refer to Justin's tutorial, you can use it for every system,
where the reaction coordinate is the distane between two parts of the
system. You probably need to make some little adjustments, but in the
end it doesn't matter if you pull two proteins apart, or protein+ligand,
2 water
I never looked into the code, but i understanded it the following way
(for pull_geometry = distane, direction, position).
For the pulling the reference group is held fixed and the force is
applied to the pulled group. Since the reference group an move during
the rest of the simulation (all
TL;DR version (longer version below):
Due to the stochastic nature of SMD (and pulling experiments in general)
it is quite natural that the results for different simulations will not
be excatly the same.
I would say you are fine. Thing is, if you do ligand unbinding SMD
simulations the
Think i now understand your question. Forget what i wrote before.
I could imagine the the 'grompp -t npt.cpt' part is a problem.
If the simulations would be numerical reproducible, one should get the
same results. As they are not, the results will differ somewhat (would
think the more, the
Don't know. One idea i have: Take a flexible and a relative rigid system
and perform simulations with the same starting conditions (- using -t
*.cpt). I would imagine that for the flexible system the trajectories
start earlier to deviate, since more stuff could happen (system is more
flexible
Yes, from 4.5.x manual:
pull_ngroups: (1)
The number of pull groups, not including the reference group. [...]
Just set 'pull_ngroups = 2' and then make entries for
pull_group1 - pull_vec1 ...
pull_group2 - pull_vec2 ...
and so on...
greetings
thomas
Am 12.04.2013 12:00, schrieb
Must get the bus, so only short answer.
You could try to use constraint pulling instead of an umbrella
potential. Then the ligand should move 1nm in 1ns. And you could see is
the setup is ok, or if it would be better to pull into another direction...
greetings
thomas
Am 07.04.2013 18:05,
The easiest solution would be using 'pull_geometry = distance' in all
three dimensions. Then you can be sure that both groups are pulled
together. Small remark: One group would be fixed for the pulling, and
the second group gets pulled towards the first group. So if you want to
have both
Look for
pull_geometry = direction_periodic
This should solve the problem.
Greetings
Thomas
Am 20.03.2013 12:00, schrieb gmx-users-requ...@gromacs.org:
Dear all,
I want to use Umbrella sampling method to calculate the potential of
mean force. Unfortunately, the distance of my two groups is
Looking into the manual, i find under the 'energy monitor group':
'Mutual interactions between all energy monitor groups are compiled
during the simulation. This is done separately for Lennard-Jones and
Coulomb terms. In principle up to 256 groups could be defined, but that
would lead to
Hi,
you use a relative high tau_t:
tcoupl = v-rescale
tc-grps = CO2 PARA PAR2
tau_t = 1.0 1.0 1.0
ref_t = 410 410 410
In my simulations i use a value of 0.1
don't know if this would help, but it was the only thing which catched
my eye, as i read you .mdp parameters.
Greetings
Thomas
Am
Am 15.01.2013 12:52, schrieb gmx-users-requ...@gromacs.org:
On 1/15/13 5:49 AM, Devika N T wrote:
HI
I would like to know the protocol to be followed for performing MD
simulation
for calcium with protein (Calmodulin)
Can I follow the same protocol which is followed for a protein?
Probably,
Am 15.01.2013 14:17, schrieb gmx-users-requ...@gromacs.org:
On 1/15/13 8:12 AM, Thomas Schlesier wrote:
Am 15.01.2013 12:52, schriebgmx-users-requ...@gromacs.org:
On 1/15/13 5:49 AM, Devika N T wrote:
HI
I would like to know the protocol to be followed for performing MD
simulation
Dear all,
i have a small question regarding the '-nosum' option of 'mdrun'.
The manual states:
For a global thermostat and/or barostat the temperature and/or pressure
will also only be updated every nstlist steps. With this option the
energy file will not contain averages and fluctuations over
I would also use the same residue from the pulling for the US.
One thing you should be aware of is the pulling dimension:
Now you have the pull-code only ativated for the z-direction. If you use
this still in the US the ion can move freely in the xy-plane (freely in
the sense of what is
Have a look there:
http://virtualchemistry.org/molecules/110-02-1/index.php
virtualchemistry.org is a really nice site (from David van der Spoel,
and others i think), which has many paramters for solvents for the GAFF
and OPLS force field. And also Physical properties for these.
Greetings
They have also the complete force field parameters under:
OPLS Auxiliary topologyoplsaaff.itp
if there are more paramters then in the oplsaa.ff directiory, then they
have probably developed these parameters.
They give this paper as a reference for the calculations. Probably
something is
This should be in the pullf.xvg (time and then the forces).
Am 24.11.2012 19:55, schrieb gmx-users-requ...@gromacs.org:
Hi to all gromacs users,
I am trying to run an umbrella sampling and i am getting the initial
conformations by pulling simulations but i want to check the simulation
A good start might be:
Phys. Chem. Chem. Phys., 2011, 13, 10437–10448
This paper is about hybrid-models (mixing CG and AA). But they discuss
'boltzmann inversion' and 'force matching', which are both methods to
obtain CG-potentials.
Since they use small molecules it focusses on nonbonded
The rdf should not depend on the choice 'which is group A and which is
group B'! Not if the system is well equilibrated and not if you consider
only a single snapshot (in that case the rdf looks like garbage if the
system is not really huge, but the RDF(A-B) and RDF(B-A) must be the same).
I
But be aware that the force depends on the pulling velocity. If you
perform the simulation with two different pulling velocities you'll get
two different forces for each distance.
The easiest way to get the force as a function of the distance (without
the bias of the pulling velocity) would be
Am 13.11.2012 06:16, schrieb gmx-users-requ...@gromacs.org:
Dear all,
i did some scaling tests for a cluster and i'm a little bit clueless about the
results.
So first the setup:
Cluster:
Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR
GROMACS version: 4.0.7 and 4.5.5
Compiler: GCC
Sorry for reposting, but forgot one comment and added it now below:
Am 13.11.2012 06:16, schrieb gmx-users-request at gromacs.org:
Dear all,
i did some scaling tests for a cluster and i'm a little bit
clueless about the results.
So first the setup:
Cluster:
Saxonid 6100, Opteron 6272
Dear all,
i did some scaling tests for a cluster and i'm a little bit clueless
about the results.
So first the setup:
Cluster:
Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR
GROMACS version: 4.0.7 and 4.5.5
Compiler: GCC 4.7.0
MPI: Intel MPI 4.0.3.008
FFT-library: ACML 5.1.0
Dear all,
i have access to a cluster on which GROMACS is compiled with a different
version of GCC and a different FFT libary (compared to the local machine).
Will this affect simulationns if i prepare the *.tpr on the local
machine and run the simulation on the cluster and the local machine?
See the SHAKE algorithm in the manual.
Especially equation (3.98)
- G_i = \sum_k \lambda_k * (\partial \sigma_k)/(\partial r_i)
where G_i is the constraint force
\sigma_k are the equations for the constraints
and \lambda_k is the lagrange multiplier
'Understanding molecular simulation' (D.
But for GMX 4.0.7 there are forces in the pullf.xvg. The forces which
arise rom the contraint the hold the two groups fixed. I use them for
thermodynamic integration...
I use the following mdp-parameters, probably this gives you an idea what
you might make different:
; AFM OPTIONS
pull
1768.6 -214.64 -199.829-2746.97
1177.7 476.39 288.535 -559.274123.08 114.493 851.86 550.558
As Thomas Schlesier mentions here,
http://gromacs.5086.n6.nabble.com/pull-constraint-gives-zero-forces-tp5001817.html,
the pullf output apparently contains the forces necessary to enforce
You could use 'constraint' pull-mode instead of the 'umbrella' mode.
Than the distance would change gradually and you won't observe the
fluctuations in the distance.
greetings
thomas
Am 04.10.2012 16:58, schrieb gmx-users-requ...@gromacs.org:
On 10/4/12 10:52 AM, jiang wrote:
Justin Lemkul
Am 23.08.2012 23:11, schrieb gmx-users-requ...@gromacs.org:
hello :
I am a little bit confused about the difference between gen_seed and
ld_seed. I checked the manual, it is said:
gen_seed
used to initialize random generator for random velocities, when gen_seed
is set to -1, the seed is
As a first step, i would shift all curves so, that the energy of the
minium is for all plots at the same (aribarity) value. The minimum
should be the point which has sampled the best. If you shift then all
values, it should be easier to spot differences between the plots.
And probably make
Since your simulations of the individual windows are about 50 ns, you
could first dismiss the first 10 ns for equilibration, and then perform
the WHAM analysis for 10-30 ns and 30-50 ns. If everything is fine, you
should see no drift.
If you want to have more data for the analysis you could
Am 21.08.2012 18:22, schrieb gmx-users-requ...@gromacs.org:
On Tue, Aug 21, 2012 at 4:49 PM, Thomas Schlesierschl...@uni-mainz.de wrote:
Since your simulations of the individual windows are about 50 ns, you could
first dismiss the first 10 ns for equilibration, and then perform the WHAM
?!?
Still not an accurate model - you'd have a CO2 with three sites and mass
only at two of the sites, so either the mass or moment of intertia must
be wrong.
Mark
Can anyone comment on this?
greetings
thomas
On 25/07/2012 10:08 PM, Thomas Schlesier wrote:
What you have done there looks very
What you have done there looks very strange...
easiest wy would be:
define the two oxygens as normal atoms (1,2), give them a bondlength
twotimes the C-O bond length
define the carbon as a dummy (3), while you construct it's position from
both oxygens with a=0.5
one thing i don't know is how
on this?
greetings
thomas
On 25/07/2012 10:08 PM, Thomas Schlesier wrote:
What you have done there looks very strange...
easiest wy would be:
define the two oxygens as normal atoms (1,2), give them a bondlength
twotimes the C-O bond length
define the carbon as a dummy (3), while you construct
As others said:
type 2 virtual site
check chapter 4.7 and 5.2.2 in the manual (version 4.5.x).
Greetings
Thomas
Am 24.07.2012 12:00, schrieb gmx-users-requ...@gromacs.org:
Sorry I should mention it at the very beginning that I have a linear
molecule and the angle is to be constrained at 180
It could be possible tht you do not pull into the 'right' direction. if
there is another group between 'GTP' and 'Residue' you will get clashes
and 'Residue' won't move further (could be a water molecule, or some
other part of 'GTP').
If this happens you should observe an increase in the force
If you want to pull along a vector which connects to groups, the easiest
way is to run 'g_dist' over your starting *.gro file.
this measures the distance and the vector connecting both groups. From
GROMACS-4.0.x you don't need to normalise the vector. So you can
directly use this vector.
Heard that RNA/DNA system could be a little trickier than proteins due
to the many negative charges.
I found somewhen a nice article about RNA simulations in general.
Probably some questions you have / will have are answered there:
A short guide for molecular dynamics simulations of RNA
As a side note:
The rupture process is a stochastic process, so a single rupture force
is meaningless, since it is a distributed property. So you need to do
many simulations to get the distribution / average rupture force.
It that same like equilibrium properties, one doesn't determine them
You have 1mol of your system.
conversition factor for
kJ/(mol*nm) - pN is approx 1.661
Am 29.06.2012 10:33, schrieb gmx-users-requ...@gromacs.org:
Dear Gmx Users,
How to recalculate the force constant from the harmonic potential: 1
[pN/A] into [kJ/mol nm2] ? Where is the [mol] here?
think you encounter the problem, that you construct your pmf from a 3d
simulation and project it onto 1d, but do no correction.
For TI (if you constrain the distance in all three directions) the pmf
is given by
V_pmf(r) = - \int [ F_c + 2/(beta*r) ] dr
with F_c the constraint force and \beta
It also depends in some cases strongly on the system.
I have a two-state system in which both states are rather narrow (doing
a normal pulling simulation, the end-to-end-distance seems nearly
constant). In these two regions one could use small force constants. but
both state are seperated by a
information on the factor in regard to TI:
E. Paci, G. Ciccotti, M. Ferrario; Chem. Phys. Letters 176, 6: 581-587, 1991
On 7/3/12 2:50 PM, Thomas Schlesier wrote:
think you encounter the problem, that you construct your pmf from a 3d
simulation and project it onto 1d, but do no correction
should also have these interactions (nonbonded and bonded) in
the *nb.itp and *bon.itp files of your force field and the atom
definition in the *.atp file.
The basic informations for both ways are in chapter 5 of the manual.
Hope this gives some hints.
Greetings
Thomas Schlesier
Am 20.06.2012
and the atom
definition in the *.atp file.
The basic informations for both ways are in chapter 5 of the manual.
Hope this gives some hints.
Greetings
Thomas Schlesier
Am 20.06.2012 16:18, schriebgmx-users-requ...@gromacs.org:
Hi everybody,
I try to use GROMACS for my protein
Hi all,
i have a more conceptional question, for using vsites as
interaction-centers for coarse-grained particles:
First the simple case:
I want to simulate one benzene molecule (atomistic - aa) in
coarse-grained (cg-) benzene (each benzene molecule as a single
particle). For the cg-cg
Dear Richard,
thanks for the idea, i will try this.
Relating to your side note:
I perform pulling simulations of a calixarene-catenane dimer (both together 600
atoms)
and i mesitylene as a solvent. To access longer time-scales I wanted to
coarse-grain the
solvent only. My supervisor said that
One comment:
If the channel is horizontal orientated, and the COM of MOL lies in the
middle, you have two directions to go out of the channel: two the left
side (quasi negative distance) and to the right side (quasi positive
distance).
What happens with 'pull_geometry=distance' is, that only
Where is the center of mass of reference group (MOL) located?
It seems that the COM is near the middle of the ion channel. Since you
use 'pull_geometry=distance', g_wham will look only for the distance
between 'MOL' and 'Na' and that leads to problem.
If the com of 'MOL' sits in the center of
I think all the answers to your question are in the tutorial. Probably
read first the lysozyme tutorial and then the umbrella tutorial again.
But here is a more general answer:
Normally you have two types of simulations:
preperation (which is also equilibration)
production
and the need of
...@vt.edu
Subject: Re: [gmx-users] Re: Wierd results from Umbrella sampling,
(Justin A. Lemkul)
To: Discussion list for GROMACS usersgmx-users@gromacs.org
Message-ID:4fbbc9bd.8070...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/22/12 6:53 PM, Thomas Schlesier wrote
Think it would be best to show the .mdp file, else we can only guess
what the parameters are.
From the histogram it looks like that the force constant of the
restraining potential is too low, since the histograms are really wide,
but pull_k1=1000 is a 'normal' value.
On thing which confueses me
I never worked with the MARTINI (or other coarse-grained) force field,
but this in the umbrella.mdp
title = Umbrella pulling simulation
integrator = md
dt = 0.019
looks suspicious. The dt is about an order of magnitude greater than one
uses in normal (bond-)constrainted
Hi,
relating to the picture see:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
It's just a matter of periodic boundary conditions, you don't have two,
but just one cluster of octanol.
What i don't understand is, that your box doesn't collapse (becoming
Am 27.04.2012 15:31, schrieb gmx-users-requ...@gromacs.org:
Hi Gmx Users,
I run umbrella sampling simulation and for one window I lost my files:
pullf.xvg and pullx.xvg.
Is there any way to extract it based on the trajectory from this window?
Steven
Should be possible, but you will be
Using the option '-com' results in a RDF were the reference group is the
center of mass (COM) of the first group.
- In a system with pure benzene and using the whole system as a group,
this reference point would be somewhere in the middle of the box. And
choosing this group twice, would result
AFAIK this factor isn't included in g_wham. Think i tested this some
years ago with an older GROMACS version.
If one looks into the 'gmx_wham.c' and searches for 'ln' one finds it
only in the comments for the gaussian random numbers.
Greetings
Thomas
Hi all
According to some references
1)
Am 18.04.2012 12:00, schrieb gmx-users-requ...@gromacs.org:
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
http://lists.gromacs.org/mailman/listinfo/gmx-users
or, via email, send a message with subject
New try, think last time message didn't reached the list :(
Original-Nachricht
Betreff: Re: g_wham problem with negative COM differences
Datum: Fri, 13 Apr 2012 14:55:15 +0200
Von: Thomas Schlesier schl...@uni-mainz.de
An: gmx-users@gromacs.org
Anni Kauko wrote:
Date
Anni Kauko wrote:
Date: Wed, 11 Apr 2012 08:38:05 -0400
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] g_wham problem with negative COM
differences
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi Gavin,
if i remember correctly it was a system about pulling a ligand from a
binding pocket?
To make the system simpler we have a big circle and in the middle a
small circle. And we assume that the potential minimum for the
interaction between both circles is when the small cirlce is in the
As far as i remember for PBC the distance between the reference and the
pulled group are relevant, and not the distance between the reference
group and the virtual spring (place where the pulling potential is zero).
Looking into the code of GROMACS-4.0.7 backs this.
If the distance between the
. The curve from the reversible work theorem
is better behaved and smoother but this could be solely due to
statistics. I am slightly confused about your statement If the small
circle moves between 0 and any value 0 everything should be fine. Do
you not mean 0 and any value 0 ? Cheers Gavin Thomas
be wrong, but would be interesting if
you got it to work like that for a small molecule.
Stephan Watkins
Original-Nachricht
Datum: Fri, 17 Feb 2012 16:34:22 +0100
Von: Thomas Schlesier schlesi at uni-mainz.de
An: gmx-users at gromacs.org
Betreff: [gmx-users] pull-code
Hi
AFAIK vdwradii.dat is only used for *genbox*. For the actual simulation
the force field paramters of CCl4 will be used.
One thing which you could check is what is the compressibility of CCl4
(the value you use reminds me as that of water) and try with this. I do
not know if the is a protocol
I assume that you energy minimisd the system, but still have atomic clashes?
One thing which helped me in a similar case, was a short simulation at
low temperature with a really small timestep (about 3-5 magnitudes
smaller than the normal timestep). With this the atoms which clashes
move away
Hi,
i second Justins seond idea (creating a small box of equilibrated CCl4
and then fill the simulation box via the -cs option).
Depending if you have other molecules in your system, make the
simulation box a little bit bigger, because you will get some holes. In
the subsequent NPT simulation
On 17/01/2012 4:55 AM, Thomas Schlesier wrote:
Dear all,
Is there a way to omit particles with zero charge from calculations
for Coulomb-interactions or PME?
In my calculations i want to coarse-grain my solvent, but the solute
should be still represented by atoms. In doing so
?
Greetings
Thomas
On 17/01/2012 7:32 PM, Thomas Schlesier wrote:
On 17/01/2012 4:55 AM, Thomas Schlesier wrote:
Dear all,
Is there a way to omit particles with zero charge from calculations
for Coulomb-interactions or PME?
In my calculations i want to coarse-grain my solvent, but the solute
Thanks Carsten. Now i see the problem.
Hi Thomas,
Am Jan 17, 2012 um 10:29 AM schrieb Thomas Schlesier:
But would there be a way to optimize it further?
In my real simulation i would have a charged solute and the uncharged solvent
(both have nearly the same number of particles). If i could
Dear all,
what is the reason, that the tabulated potential must go till r_c+1 (r_c
= cut-off radius) and not only up to r_c?
I think we only calculate the interactions till r_c and truncate the
rest. So everything behind r_c would be redundant information (due to
the truncation it would be set
Dear all,
Is there a way to omit particles with zero charge from calculations for
Coulomb-interactions or PME?
In my calculations i want to coarse-grain my solvent, but the solute
should be still represented by atoms. In doing so the solvent-molecules
have a zero charge. I noticed that for a
Dear all,
first of all, sorry to this rather conceptional question, which is not
totally to GROMOACS related. But probably anyone of you can help.
In my simulations I use mesitylene as a solvent. In future i want to
coarse-grain the full atomic mesitylene to an effective one-particle.
For
I think that for the histogram all contribution with a negative sign
would be add to the contributions from positive distances. If your
distribution is be a perfect gaussian with zero mean, you would end up
with half a gaussian with double high (for positive distances) and zero
for negative
The histograms are really crowded, it would be better to plot only the
black one and probably the red one, to see the it better.
Two ideas which can probably solve the problem (ok, both assume, that
the host has a certain shape).
You said you investigate guest-insertion to a host. I would
Dear all,
i would like to know if it is possible to get the rdf between the center
of mass of a molecule and individual atoms of said molecule?
In my case i have mesitylene and i would like to calculate the RDF
between the COM and the Methyl-carbon-atoms.
My problem is that i would need the
Hi all,
for a publication i want to list the used OPLS parameters for the
investigated molecules. In GROMACS all atomtypes are uniquely defined by
the atomtype `opls_xyz`. And from the atomtypes one can deduct the
bonded parameters. So it is sufficient to list only the atomtypes and
probably
If you use constraints it would not be umbrella sampling, where you need
to sample around a restraint structure to get the histograms for WHAM or
another analysis-technic.
So if you want to do umbrella sampling either make to box bigger and/or
make the restraints harder.
But you can also use
never used the -dist option, but i think you have here a missunderstanding:
t: 275 20230 SOL 62618 OW 0.341434 (nm)
i think this means: at time=275 atom 62618 (which is a OW) from residue
20230 (which is a SOL) is 0.341434nm away from your protein atom.
the x SOL y OW means not the
Hi all,
is it possible to mirror a trajectorie?
I have done pulling simulations, where i first pulled two molecules
apart and later used the pulled them together (starting form the last
frame of the pulling-(apart)-simulation).
Now want to calculate the rmsd of structures for the path. So i
Message: 5
Date: Tue, 15 Mar 2011 07:17:28 -0700 (PDT)
From: Michael Brunsteinermbx0...@yahoo.com
Subject: [gmx-users] pull forces
To: gmx usersgmx-users@gromacs.org
Message-ID:613152.30411...@web120517.mail.ne1.yahoo.com
Content-Type: text/plain; charset=us-ascii
Dear all,
does anybody know
hi all,
i'm trying out GROMACS 4.5.3
i'm simulating (sd-integrator) a small rna hairpin in vacuum, without
pbc for 100ps. System has about 380 atoms.
If i do the simulation a second time (grompp + mdrun) i get identical
results.
first i had only *gen_seed = -1* but latter i set also *ld_seed =
ok, problem solved...
used same .tpr file all the time
should stop working for today :)
greetings
thomas
On 02/22/2011 08:49 PM, Thomas Schlesier wrote:
hi all,
i'm trying out GROMACS 4.5.3
i'm simulating (sd-integrator) a small rna hairpin in vacuum, without
pbc for 100ps. System has about 380
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