have which values set for the A and B states.
On Wed, Oct 30, 2013 at 5:36 PM, Dallas Warren wrote:
> Michael, thanks for taking the time to comment and have a look.
>
> The real issue I am having is a bit deeper into the topic than that, my last
> reply was just an observation on some
I think the grammar got a little garbled there, so I'm not sure quite
what you are claiming.
One important thing to remember; 1-4 interactions are treated as
bonded interactions right now FOR COUPLE intramol (not for lambda
dependence of the potential energy function), so whether
couple-intramol i
Not that many people have used this
code, thus there are likely ways that it can be improved for better
utility. I generally haven't tried to calculate free energy
differences from the transition matrix, though it should give
consistent results with the other methods.
Best,
~~~~
Hi, all-
Rest essentially scales the solute-solvent interactions, but maintains
the solute-solute interactions. This can be done solely with
Hamiltonian replica exchange, which is in 4.6. It's a bit tricky,
though. We plan on having something that does this automatically in
5.0 or 5.1, but it's
Hi, all-
At this point, any fixes are going to be in the 5.0 version, where the
integrators will be a bit different. If you upload your system files
to redmine.gromacs.org (not just the .mdp), then I will make sure this
gets tested there.
On Fri, Oct 25, 2013 at 10:14 AM, Guillaume Chevrot
wrot
Is there a link to the documentation? It's a little difficult to know
exactly what this supposed to be doing. Is it a GUI interface to
gromacs?
In general, it would be great to get these sort of extensions
coordinated with the main gromacs development tree, since otherwise
they would tend to get
Hi, Guillaume-
No one can tell you if you did anything wrong if you didn't tell us
what you did! There are literally thousands of combinations of
options in running an NVE simulation, a substantial fraction of which
are guaranteed not to conserve energy.
If you post the files (inputs and relevan
OPLS-AA was generally derived with Monte Carlo, which means that all
bonds were exactly constrained. But read the papers!
On Thu, Oct 10, 2013 at 12:27 PM, Justin Lemkul wrote:
>
>
> On 10/10/13 12:17 PM, Martin, Erik W wrote:
>>
>>
>> Hi, I'm new to both Gromacs and OPLS. I have always used CH
Zidar wrote:
> Dear Michael.
> The simulations at each lambda point starts from the same structure
> that I equilibrated (NPT ensemble) for 20 nanoseconds. The system has
> ~7500 atoms in a box the size 5 nm x 5 nm x 5 nm. The molecule of
> interest is located in the center of the u
Sounds like the simulation is blowing up. How soon does it start crashing.
Also, what configurations are you using to start your free energy
simulations at each lambda?
On Wed, Oct 2, 2013 at 10:31 PM, Jernej Zidar wrote:
> Hi all,
> I'm trying to determine the free energy of solvation for a
Hi, Chris-
The best place to file this issue is the SimTK pymbar page, rather
than alchemistry.org, since it's a pymbar problem.
We have collaborators that may have updated the pymbar.py recently.
I'll try to get this stabilized in the very near future.
Testing quickly, my best guess is that it'
ility outlined above.
>
> Thank you for your assitance Mark and Michael.
>
> Chris.
>
> -- original message --
>
> Michael Shirts mrshirts at gmail.com
> Fri Sep 27 00:41:17 CEST 2013
> Previous message: [gmx-users] segfault when running the alchemistry.org
>
energy calculation pathways, the
sc-r-power=48 pathway will now be phased out anyway by 5.1.
On Thu, Sep 26, 2013 at 6:37 PM, Michael Shirts wrote:
> I thought I had just managed to solve the issue :)
>
> If you look at the soft core parameters, there are two types listed --
> one wit
I thought I had just managed to solve the issue :)
If you look at the soft core parameters, there are two types listed --
one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power
are more stable with single precision calculations.
I have changed the files on the website to make the
Just to be clear, is this the expanded ensemble version of the calculation?
On Thu, Sep 26, 2013 at 5:25 PM, Mark Abraham wrote:
> I found the -multi version of that tutorial a bit temperamental...
> Michael Shirts suggested that double precision is more reliable for
> expanded
There are some starter files here:
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_free_energy_calculations%3a_Michael_Shirts%2c_Session_2A
Which can be used in conjunction with the Alchemistry.org instructions.
But it needs to be update
The only integrators with stochastic force components are sd and bd.
vrescale has a small stochastic component, but that is for the target
kinetic energy, and is not a random force acting on each particle.
On Thu, Aug 29, 2013 at 3:15 PM, Ali Sinan Saglam
wrote:
> Hi,
>
> I was planning to use t
IPS in CHARMM involves additional calculations beyond a simple
homogeneous approximation -- roughly equivalent to PME for dispersion,
though its a bit messier.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723858/
On Thu, Aug 29, 2013 at 7:56 AM, Justin Lemkul wrote:
>
>
> On 8/29/13 1:18 AM, G
Can you clarify - Do you mean that different replicas have different
average pressures?
WITHIN each replica, the +/- 2000 bar changing from step to step is
very common for using an atomic virial like gromacs does.
The AVERAGES of EACH replica should each be the average pressure they
are set as (+
Pressure should fluctuate significantly. The estimator for the
pressure that is generally used is very noisy. The question is, do the
pressure averages over, say, 500 ps or 1 ns look about right?
On Sun, Aug 25, 2013 at 5:07 PM, Mark Abraham wrote:
> On Sun, Aug 25, 2013 at 6:22 PM, rahul seth
>
able to us. Thank you.
>
>
> On Tue, Aug 20, 2013 at 10:50 AM, Michael Shirts <
> michael.shi...@virginia.edu> wrote:
>
>> Dear GROMACS users-
>>
>> I'd like to remind you all about the 2013 GROMACS USA Workshop and
>> Conference at the University of Virgini
,
The 2013 GROMACS USA Workshop and Conference Steering Committee
Michael Shirts (chair)
Angel Garcia
Berk Hess
Yu-Shan Lin
Erik Lindahl
Peter Kasson
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I don't go beyond 2 fs with either all- bonds or h-bonds. Things like kinetic
energy start being subtly off.
H-bonds has less chance of failing with large numbers of constraints- less
iteration required, especially if bond system cross parallelization boundaries.
If your molecules are < 10 atom
This is a plumed error, not a gromacs error. Gromacs never handles those
keywords.
Sent from my iPhone
On Aug 14, 2013, at 1:40, Albert wrote:
> Does anybody have any idea what's the problem?
>
> I use the tutorial example and I don't know why it doesn't work.
>
> THX
>
>
> On 08/13/2013
This is
Sent from my iPhone
On Aug 14, 2013, at 1:40, Albert wrote:
> Does anybody have any idea what's the problem?
>
> I use the tutorial example and I don't know why it doesn't work.
>
> THX
>
>
> On 08/13/2013 07:19 PM, Albert wrote:
>> Dear:
>>
>> I am trying to run plumed with gromac
Hi, Sanku-
The way to invoke Hamiltonian replica exchange has changed to be a bit
more flexible. We should go back and make sure that this legacy way
is supported (I thought this invocation was supported, but apparently
it isn't), but what you should be able to do to get it working quickly
is inc
>> be the "best" version ;)
>>>>>
>>>>> -Justin
>>>>>
>>>> Hi Justin,
>>>>
>>>> I just tried it with version 4.6.3. and rlist=rcoulomb=rvdw = 0.
>>>> Unfortunately,
>>>> I get
that in the position restraint case (not COM-pulling), where
> the reference positions are determined by the starting structure instead of
> a B-state topology, the reference positions won't be swapped ?
>
>
> 2013/8/3 Michael Shirts-2 [via GROMACS] <
> ml-node+s5086n50
Short answer is anything that has a B state parameter can be included
in in Hamiltonian exchange.
If it's pull code or explicit restraints, it's controlled by restraint lambda.
> I went through the manual and couldn't find any definite answers to the
> following questions.
>
> First, I wonder if
Hi Dejun-
The basic problem is that for this particular configuration, the
current state is the only state with nonzero weight. Note that the
state with the second highest weight has weight 10^-7. When it tries
to compare weights in single precision, it has a numerical overflow
and fails.
A few
p and Conference Steering Committee
Michael Shirts (chair)
Angel Garcia
Berk Hess
Yu-Shan Lin
Erik Lindahl
Peter Kasson
Original announcement:
~~~
We are pleased to announce the 2013 GROMACS USA Workshop and
Conference at the University of Virgin
Problem partly addressed. If I run normal modes in -nt 1, then I get
the same force as after the minimization.
I'll file a redmine.
On Sat, Jul 20, 2013 at 9:43 AM, Michael Shirts wrote:
> To follow up -- if I try to minimize again using -t, I get the same
> low forces as in the m
To follow up -- if I try to minimize again using -t, I get the same
low forces as in the minimization in the previous step. So it appears
to be something with what do_nm is doing, not with errors in the
output structure.
On Sat, Jul 20, 2013 at 9:37 AM, Michael Shirts wrote:
> When I minimiz
When I minimize a structure, I can get down to the force max being <0.01
Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
Potential Energy = -5.12340607768673e+03
Maximum force = 6.68907856457542e-03 on atom 3029
Norm of force = 2.19978176343026e-03
kJ/nm. However, whe
Chris, can you post a redmine on this so I can look at the files?
Also, does it crash immediately, or after a while?
On Thu, Jul 18, 2013 at 2:45 PM, Christopher Neale
wrote:
> Dear Users:
>
> I have a system with water and a drug (54 total atoms; 27 heavy atoms). The
> system is stable when I
dG values although
> it's not optimal for data collection as you pointed out. I wonder if it's a
> trivial fix that might have been done to add semiiso to MTTK?
>
> Thanks again for your help!
>
>
> 2013/7/17 Michael Shirts
>
>> > It seems to have something t
> It seems to have something to do with the integrator/pressure-coupling.
that is what I expected based on some preliminary testing earlier.
When
> I ran the tutorial on
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble,
> everything seems fine
OK go
4.5.7 does not support Hamiltonian exchange. It says all properties
are the same, because all the temperatures and pressures are the same
-- it won't switch the umbrellas.
On Wed, Jul 17, 2013 at 3:30 PM, Parisa wrote:
> Hi Michael,
>
> I think that this is an issue with the gro
Ah, this is a force field issue -- urey-bradley terms are not
supported free energy calculations. However, since only restraints are
changing, this warning doesn't really need to be there.
It would be relatively simple to put in a check to allow this to work,
but it might take a week or two to get
- I'd have
to dig a bit to get you good results on that . . .
On Tue, Jul 16, 2013 at 3:19 PM, Dejun Lin wrote:
> Hi Michael,
>
> Thanks for the reply. Just a quick follow-up. Do you think the overlap of
> energy histogram between different lambdas matter for lambda-dynamics in
&g
You need to have different pull parameters at the end states. Right
now, pull-kB1 is not defined in your code, so there is nothing to
interpolate to: it assume pull-kB1 = pull-k1.
Longer scale -- one would want to define reference distances that
change with lambda within the same simulation, but l
Hi, all-
This not a problem with W-L, but is instead something that is wrong
with a particular combination of mdp options that are not working for
expanded ensemble simulations. W-L can equilibrate to incorrect
distributions because it decreases the weights too fast (more on that
later), but that
Have you checked out the -ndec option for trjconv? If you have a high
precision format (.trr, or .xtc if they are stored with sufficient
precision) you can print out a .gro file (that gromacs can read) with
higher precision.
Gromacs can read .gro files with increased precisions in the
coordinates
No.
This is a statistical mechanical issue, not a GROMACS issue. For
interacting systems, entropy is a quantity describing the system as a
whole, and cannot be defined for different parts of the system, at
least not in any way such that the individual components can be added
together.
I'm also n
Hi, Sonia-
Gromacs 4.6.2 (some bug fixes vs 4.6.1) with the example files you
point out from Alchemistry.org should work well for expanded ensemble.
David Mobley and I have been validating expanded ensemble and replica
exchange, and the files posted there now are stable for all sizes of
systems,
> or should i be doing < U+*ref_p > = ?
More specifically, + *ref_p = H
isn't really meaningful thing. I mean, you can define something
such that = H, but that's not really thermodynamics.
> example system gives = -1168 kJ/mol and i find = -725 kJ/mol either
Interesting. What material at
and Conference Steering Committee
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Angel Garcia
Berk Hess
Yu-Shan Lin
Erik Lindahl
Peter Kasson
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If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.
The "pressure" quantity calculated from the KE and the virial is not
the pressure. It is a quantity that when averaged over time is equal
the pressure. Only the average is meaningful macroscopically.
An important final point is that you can always see EXACTLY what
grompp is putting into the B state by running gmxdump on the resulting
tpr. It's a LOT of information, but all in text all the interactions
are listed explicitly there.
On Mon, Jun 10, 2013 at 6:20 PM, Justin Lemkul wrote:
>
>
> On
> It should also be noted (and obvious now that I actually look into it) that
> using dispersion correction results in both the latent heat of vapourisation
> and density of the alkanes being over estimated (for both Cut-off and
> Reaction Field, and by the same amount).
That may not be quite t
that are solved by NH chains are for small toy
systems.
On Sun, Jun 2, 2013 at 2:17 AM, James Starlight wrote:
> Michael,
>
>
> thanks for suggestions.
>
> the main reason of ussage N-H with chains is the assumption that simple N-H
> does not provide ergodicity of the system
I can't think of any instance where nose-hoover chains provides an
advantage over nose-hoover in a large system -- all the demonstrations
of superiority are in model systems that are not particularly chaotic.
As the system gets more chaotic, it matters less.
I would go with md, nose-hoover (w/o c
Hi all
I am doing an NVE simulation of a protein immersed in water, and I want
to keep track of the potential energy in the protein. Do you know how can I do
it?.
I tried saving the energy of the protein ( the protein as an energy group) in
the .edr file, but when I checked the file with g_en
Summarizing!
On Fri, May 3, 2013 at 12:31 AM, XAvier Periole wrote:
>
> Are confirming that you reproduce the problem with gmx-4.6.1 or simply
> summarizing in case we lose track :))
>
> On May 2, 2013, at 23:31, Michael Shirts wrote:
>
>> So to summarize -- the pr
I
> turned it off during compilation …
>
> You could try to run on particle decomposition to see if you get a problem …
> it should one quite quick.
>
> On May 2, 2013, at 2:36 PM, Michael Shirts wrote:
>
>> Both. So if 4.6.1 doesn't work, I want to know so we
l try gmx-4.6.1
>
> On May 2, 2013, at 2:26 PM, Michael Shirts wrote:
>
>> Quick check here -- is 4.6 behaving correctly? I actually spent some
>> time working on REMD in 4.6, and it seems to be behaving correctly in
>> my hands with temperature and pressure cont
Quick check here -- is 4.6 behaving correctly? I actually spent some
time working on REMD in 4.6, and it seems to be behaving correctly in
my hands with temperature and pressure control.
Thanks for any additional info on this!
On Thu, May 2, 2013 at 8:18 AM, Mark Abraham wrote:
> On Thu, May 2
are based on different force fields.
What can I do to fix the problem?
I can change the drug if it is necessary, any drug avaliable in OPLS?
thanks for your help
John Michael
Indiana University
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You have to change atom types. For example:
[ atomtypes ]
;name bond_typemasscharge ptype sigma epsilon
h1h1 0. 0. A 2.47135e-01 6.56888e-02
h1_pert h1 0. 0. A 2.47135e-01 3.56888e-02
; perturbed
The
more general multistate lambda vector formalism for 5.0.
If you have suggestions, let me know.
I'd be happy to look over input files or give additional advice on a
specific setup.
On Tue, Apr 2, 2013 at 12:52 PM, Dejun Lin wrote:
> Hi Michael,
>
> Do the codes now support walk
Great -- if it doesn't seem to be working the way it should after some
playing around, then submit it as a redmine issue, and I'll take a
look.
On Fri, Mar 8, 2013 at 2:51 AM, Joakim Jämbeck wrote:
> Dear Michael,
>
> Thank you for your reply.
>
> Yes, it is relative
Hi, Joakim-
Hamiltonian exchange only should work if there is a lambda coupling
parameter that defines the potential at each state. You need to
define your pulling potential so that the coupling-lambda parameter
can be used to define the different pulling location centers along
your trajectory.
There is no theoretical reason to exclude it. The CMAP code is routed
differently in the logic, and was put in at the same time the free
energy code was, so it's just software engineering issues.
This is a good candidate for inclusion in 5.0 if enough people request.
On Wed, Feb 27, 2013 at 1:04
My personal opinion is that for large protein-protein calculations,
the free energy should be computed through potential of mean force
calculations, NOT alchemical methods, using the endpoints (properly
corrected) to determine the free energy of association.
There are a number of tutorials and exa
Ah, now perhaps I see that I misread the question - it could have been
phrased more clearly. If Erik understood it correctly, then the
answer to the question is: It depends on the integrator. The
simulation is not constrained to a particular temperature or pressure
- rather, the dynamics are modi
The coordinates and velocities that are printed (and that are used to
calculate the properties like energy, virial, etc) are always
consistent with the constraints. The exact order of how things are
done often depends on the integrator. For example, velocity scaling
can be done before or after co
Hi, Joakim-
Expanded ensemble is still a bit experimental. I don't immediately
see any problem that jump right out, but if you go to
http://redmine.gromacs.org/ and file a bug report, including giving
example files that cause the problem, I can take a look at it.
On Tue, Feb 5, 2013 at 6:00 AM,
I assume PLUMED will be implemented for Gromacs 4.6, as many PLUMED
developers use Gromacs. Perhaps any PLUMED lurkers on the list can
speak up. . . .
On Wed, Jan 16, 2013 at 9:20 AM, Mark Abraham wrote:
> The GROMACS team has no plans for that. The usual problem here is that
> everybody would l
> Could you tell me is there any difference of different Tau_t ussage (
> inverse friction in case of Stochastic dynamics) for simulation of
> water-soluble as well as membrane-proteins ? In the first case I'm
> using tau_t 2ps that is lower than internal water friction. In the
> second case one pa
Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala Un
> In the absence of PBC, you simply have an infinite system. In a loose
> sense, that may be NVT, but V is infinite, so whether or not you can
> consider that to be constant or not is theoretical math above what I know :)
A real molecule in vacuum is usually NVE -- it is not coupled to the
enviro
Hi, all-
I would recommend using Parrinellio-Rahman + Nose-Hoover md + at least
until 4.6.
A random-walk drift in the conserved energy is actually what MTTK
gives -- it's not as conserved as, say, energy conservation, it just
has an expectation value of zero drift over time, which means that the
It's in review with JCTC right now.
On Thu, Nov 22, 2012 at 2:19 PM, ABEL Stephane 175950
wrote:
> Hello,
>
> This is a very nice and interesting work, Michael. Thank you for the efforts
> you made in writing this paper. I hope you will publish it.
>
Hi, all-
There are some issues with MTTK + constraints that are being worked
out for 4.6. The good thing is, I have developed some sensitive tests
of the correct volume distribution (see
http://arxiv.org/abs/1208.0910) and the errors in PR are very, very
small. I would recommend using md + PR for
Michael Espinosa-Duran
PhD Student in Chemical Physics
Indiana University
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> However, the time value (4 in this example) is limited to 6 digits.
Sounds like this should be increased? There's a pending change to
replica exchange, so this could be added to 4.6 without disrupting the
release timing.
On Wed, Sep 26, 2012 at 11:22 AM, Andreas Zink wrote:
> Dear all,
>
> I
up tweaks, but let's start with 4.5 scaling info!
Best,
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shi...@virginia.edu
(434)-243-1821
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I've done some extensive testing (paper on testing method in the
works) and vrescale gives a very accurate ensemble very well for NVT.
Parrinello-Rahman and MTTK are the only algorithms that are correct
for NPT. Berendsen barostat is not. Note that there is a bug with
vrescale + md-vv + that is f
(?), but we can plan now. Note that withe errors this
big, 100-200 ps should be enough to see what's going on, so it can be
done rapidly. Drop me a line off the list to figure out details?
Best,
Michael
On Fri, Aug 24, 2012 at 9:22 AM, David van der Spoel
wrote:
> Hi,
>
> we have terrib
n, it will be possible
to parameterize lipids that behave correctly.
Best,
Michael
On Sun, Aug 19, 2012 at 3:16 PM, David Ackerman wrote:
> Hello,
>
> I was wondering when it is appropriate to use Dispersion Correction
> for lipid bilayers, or which setting (no, EnerPres, or Ener) is
Hello All -- I'm trying to do a normal modes analysis of a fairly
large crystal system (~20,000 atoms) in double-precision GROMACS. The
system is xy periodic with 2 9-3 walls, and has periodic molecules. I
first minimized the structure with L-BFGS to 1e-5 tolerance with
switched vdW interactions an
ncy than the nonbondeds, which will be another useful way to get
longer times steps. We also have planned to implement a Monte Carlo
barostat, which will give exactly the correct NPT distribution for any
integrator.
Best,
Michael
On Fri, Jul 27, 2012 at 2:01 PM, Katie Maerzke wrote:
> Hi all -
&
The implementation of BAR in gromacs is pretty hard for me to follow
because of how everything is stored noncompactly in the histogram. In
4.6, both can be computed from the same dhdl.xvg file, so it might be
easier to track down possible bugs.
On Fri, Jun 29, 2012 at 2:24 PM, David van der Spoel
her in terms of methods nor
references)
I don't know what P. H. Hünenberger said in his talk, but i am mostly concerned
about correction terms discussed here: J. Phys. Chem. 1996, 100, 1206-1215
thanks,
michael
===
Why be happy when you could be normal?
--
g
t now constraints are not applied to waters at all (O and
H look as if they move independently)
it also didn't help renaming the water molecule, residue and atom names ...
any suggestions on how i can apply atom-based cut-off with lincs or shake to
water?
thanks
eparate calculations (mutation in vacuum and mutation in
solvent)
compare?
cheers
michael
===
Why be happy when you could be normal?
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id
here ? if this is so
it might be a good idea making g_bar read tpr files to give a warning in such a
case ...
i guess for now i'll wait for a stable 4.6 - any ideas when this will be there?
thanks!
michael
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hi
as suggested in: http://www.gromacs.org/Developer_Zone/Roadmap/GROMACS_4.6
i do:
prompt> git clone git://git.gromacs.org/gromacs.git
Cloning into 'gromacs'...
remote: Counting objects: 119131, done.
remote: Compressing objects: 100% (21428/21428), done.
remote: Total 119131 (delta 100642), re
Hi,
i just performed a free energy TI calculation, to get the
free energy of solvation of water in water (the chemical potential of water)
i stuck closely to the templates given in the tutoral by justin lemkul.
The final result i get with g_bar looks good, and the number is within the
error-bars
s for any advice!
michael
mdp:
integrator = sd
nsteps = 10
dt = 0.002
;
pbc = xyz
nstcomm = 100
comm_grps = System
;
nstxtcout =
0
nstenergy = 100
ns
It only matters for running on Folding@Home. For other users of
gromacs, it doesn't do anything.
On Tue, Jun 26, 2012 at 3:50 PM, Bao Kai wrote:
> Hi, all,
>
> I am wondering what the --enable-fahcore option of configure means. I
> got the explanation from configure --help of "create a library
There's a fair amount of interest for more general support for Monte
Carlo methods in GROMACS 5.0. However, there is no any current
support for configuration bias Monte Carlo (or any other kind of MC)
currently in the code.
On Fri, Jun 1, 2012 at 12:10 PM, Benjamin Haley wrote:
> Hello,
>
> I
Gromacs already supports replica exchange -- what particularly are you
implementing?
Equilibration of pressure is always a good idea -- even if you are
running NVT simulations, you want to get them to be at the equilibrium
volume for your system and temperature choice, which will require
equilibra
nks
Michael Plazzer
Applied Physics, School of Applied Science
RMIT
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unless I can reproduce the error you are describing out of the box,
its unlikely I will be able to find it.
Additionally, it would be easiest if the files were deposited as a
redmine bug report, so that the information is centrally located.
Best,
Michael
On Thu, May 10, 2012 at 12:23 PM, francesco
Sabine, thanks for filing it in redmine! Having a record helps a lot.
Can you also attach all your input files to the redmine filing? It
can only really be debugged if the input files you used are included.
Best,
Michael
On Fri, Mar 23, 2012 at 9:11 AM, Justin A. Lemkul wrote:
>
>
&g
system
so problems are documented. I'm also working on the updates to free
energy code in 4.6, so I want to make sure this will be solved there
as well.
Best,
Michael
On Fri, Mar 23, 2012 at 7:16 AM, Sabine Reisser wrote:
> Hi Mark,
>
> with FE, without PR : same error
> without FE
> It also depends whether or not you use constant pressure, in which case it
> makes sense to increase the time to long enough to let the volume relax.
> I still do not understand why people do NVT REMD, because it makes all but
> one replica have a pressure that is not the ambient pressure.
If al
ACS manual, online tutorials etc.
Can anybody help me with this problem or guide me to appropriate tutorial.
Thanks in advance.
Michael
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Hi everyone. I'm doing a simulation in gromacs using the charmm36 parameters
from the gromacs website. The parameters don't seem to have carbohydrates,
which are part of the charmm36 force field. In particular, I need parameters
for trehalose. Is there anywhere I can find these parameters in a
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