You want to switch to sd instead of md.
On Oct 29, 2013, at 17:43, Vivian ww...@bu.edu wrote:
Hi GMX Users,
I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin
and it's a implicit model. My mdp file for pulling is shown as following.
integrator =
Try cgmartini.nl
On Oct 16, 2013, at 10:29 PM, 朱文鹏 jasonzhu...@gmail.com wrote:
Dear GMX users,
I am going to do some coarse-grained simulations in which the lipid
bilayeris covered by
polysarccharide. I remember the website of Martini Force Field (http://md
.chem.rug.nl/cgmartini/)
Yes it is a pity!
But particle decomposition helps :)) well helped!
It's a shame that long distance restraints limit the parallalization so much,
but it is understandable. Thanks for helping me with this.
Chris.
-- original message --
Initializing Domain Decomposition on 8 nodes
Hi Chris,
I mentioned that PS would have helped! I am sorry about the confusion. I should
have been more clear. I guess you have not followed the particle decomposition
threads lately :))
The PD option has been associated some serious issues lately … notably I
noticed it does not work well
Interactions will be off, especially the bonded terms.
On Oct 15, 2013, at 7:21, Mark Abraham mark.j.abra...@gmail.com wrote:
Also, the precision was selected when the xtc file was written, ie in the
mdp file.
Mark
On Oct 15, 2013 3:24 AM, Justin Lemkul jalem...@vt.edu wrote:
On
Could you try to reduce the nstcalcenergy flag from 100 to 10 and then one?
Similar flags apply to temperature and pressure and I believe might seriously
affect energy conservation.
XAvier.
On Oct 12, 2013, at 0:50, Mark Abraham mark.j.abra...@gmail.com wrote:
Didn't see any problem in
BG CPUs are generally much slower (clock whose) but scale better.
You should try to run on 64 CPUs on the Blue gene too for faire comparison.
The number of CPUs per nodes is also an important factor: the more CPUs per
nodes the more communications needs to be done. I observed a significant
Well use a regular plotting software and look at it or do some more elaborated
operation in or out the software to estimate the overlap :))
On May 17, 2013, at 1:14 PM, bharat gupta bharat.85.m...@gmail.com wrote:
Dear Sir,
I ran the REMD simulation with temp. distribution discussed in my
What do you not like in your distributions? What are your looking for in these
distributions?
I am not sure what you are expecting from the list here … your distributions
are fine, but, as Mark noted, it does not mean your simulation and sampling
will be optimal …
On May 17, 2013, at 3:51
, XAvier Periole x.peri...@rug.nl wrote:
The interval between the exchange trial affect the efficiency of REMD but
not the the exchange ratio (at least in principle).
In you case I am not sure what the plot are showing! Are these showing all
the replicas? what are the units?
On May 14, 2013
You have to convince yourself, not me :)) But I can give you my opinion …
On May 16, 2013, at 10:33 AM, bharat gupta bharat.85.m...@gmail.com wrote:
Okay Sir, I will try two-three combinations this time and will report back
to you ...
On Thu, May 16, 2013 at 5:25 PM, XAvier Periole
the further runs and anlysis ??
So, is it fine to continue with the third simulation ?? But still the
problem is that I am not getting the exact graphs with xmgrace??
On Thu, May 16, 2013 at 5:36 PM, XAvier Periole x.peri...@rug.nl wrote:
You have to convince yourself, not me :)) But I
Do you need it in the code? g_traj would help you do that on the trajectory.
On May 17, 2013, at 3:17 AM, Sikandar Mashayak symasha...@gmail.com wrote:
Hi
I want to store Z coordinates of atoms at the beginning of each time step
when I am doing 'mdrun -rerun'. I am not able to find the
Well, a linear 80aa peptide will need that much water anyways!
The question is more how relevant and realistic is such a structure and how
long the peptide is going to keep it? You could resolvate it after some time,
reducing the box, you could also start by a vacuo simulation to help colapse
what could be wrong in this case?? Is it the mdp file settings or implicit
solvent setting. Does the time to replica to exhange also affects their
swapping ??
On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote:
You need to increase the temperature gaps indeed if you
You may have created large files and thus got out of quota on the disc.
Check your quota and consider reducing the frequency of saving coordinates.
On May 13, 2013, at 9:46, Sainitin Donakonda saigr...@gmail.com wrote:
Hello,
I am trying to run 20 ns protein ligand simulation on cluster
, 2013, at 1:01 PM, XAvier Periole x.peri...@rug.nl wrote:
I finally could reproduce the problem in gmx461 and have fled up a red mine
report.
I hope we can fix this easily but I am not sure how things go go from now!
Someone will get the bug assigned and fix it when ever possible
You need to increase the temperature gaps indeed if you want acceptance ratio
~0.2/0.3. But again this won't work with the water …
It is not clear what happens in your index file but probably a problem from
grace to plot so many points … you can try to increase the Max drawing path
length in
.
https://www.dropbox.com/s/uvwsdqjix49lg93/remd_index.png
https://www.dropbox.com/s/78vcnaxzpgeekti/remd_temp.png?m.
On Sat, May 11, 2013 at 12:04 AM, XAvier Periole x.peri...@rug.nl wrote:
The replicas seem indeed to have exchange. Using a colour for the #
replicas would
432.83
7 464.14
8 497.24
9 532.26
10 569.32
11 608.51
according the above equation c should be somewhere around 2.37.
On Sat, May 11, 2013 at 11:10 PM, XAvier Periole x.peri...@rug.nl wrote:
Well, actually things do not look so good. But is it possible that grace
is actually
://www.dropbox.com/s/sgpblcdg9zh7f52/remd_temp.png
https://www.dropbox.com/s/6hvqlqmu64mb2jy/remd_index.png
I want to that if I include water for the simulation, the same temp.
distribution would work or not ??
On Sun, May 12, 2013 at 12:10 AM, XAvier Periole x.peri...@rug.nl wrote:
You
The replicas seem indeed to have exchange. Using a colour for the # replicas
would help.
I could not access to the first link.
Note also that the increase of exchange ratio with the temperature suggest the
distribution of the temperature is not optimal and may be with regular
intervals? You
, 2013, at 10:15 PM, XAvier Periole x.peri...@rug.nl wrote:
I'll look at the 4.6.1 version next week, I could install it but I got a
conflict between the environmental variable defining openMP variable but I
turned it off during compilation …
You could try to run on particle decomposition
You could define a repulsive potential that would apply to water molecules. I
am not sure how it is called but it is available and described in the manual.
On May 4, 2013, at 2:46, Christopher Neale chris.ne...@mail.utoronto.ca wrote:
Dear users:
I am interested in running simulations of
to analyze or
post-process this?
On Wed, May 1, 2013 at 11:11 AM, Sikandar Mashayak
symasha...@gmail.comwrote:
Thanks Xavier,
I will give it a try.
On Wed, May 1, 2013 at 10:56 AM, XAvier Periole x.peri...@rug.nl wrote:
Well I am not the expert. O.H.S. Ollila, M. Louhivuori and E
think it is a problem of equilibration.
2013/5/1 XAvier Periole x.peri...@rug.nl
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water
:
On Wed, May 1, 2013 at 10:24 PM, XAvier Periole x.peri...@rug.nl wrote:
Ok here is my current status on that REMD issue.
For info: I use
Temperature: v-rescale, tau_t = 2.0 ps
Pressure: berendsen, tau_p = 5.0 ps,
time step: dt=0.002 - 0.020 fs,
COM removal on for bilayer/water separately
, but temperature, volume, potential
energy, pressure seem all to be around normal fluctuations.
2013/5/2 XAvier Periole x.peri...@rug.nl
Did you look at some data like temperature/pressure/box size/Epot as a
function of time and especially around some exchanges?
Your system
I mean tpr files not tar! Autocorrection is sometimes funny :))
On May 2, 2013, at 2:11 PM, XAvier Periole x.peri...@rug.nl wrote:
Could you send me a set of tar files that I could look at things the same way
I do with my system? I would guess that 6 tar files where you same energies
with temperature and pressure control.
Thanks for any additional info on this!
On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com wrote:
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
, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote:
Both. So if 4.6.1 doesn't work, I want to know so we can patch it
before 4.6.2 comes out. If it does work, then there is probably stuff
that can be backported.
On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote
.
On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote:
Both. So if 4.6.1 doesn't work, I want to know so we can patch it
before 4.6.2 comes out. If it does work, then there is probably stuff
that can be backported.
On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl
AM, XAvier Periole x.peri...@rug.nl wrote:
You mean working with or working on the code?
I'll try gmx-4.6.1
On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote:
Quick check here -- is 4.6 behaving correctly? I actually spent some
time working on REMD in 4.6
The use of the original code is quite straightforward, the post processing is a
bit more confusing but quite accessible.
We have been using this code (the one available on the site) and related
version in the lab and we definitely would find it very sad to not keep this
feature available in
Lemkul jalem...@vt.edu wrote:
On 5/1/13 5:12 AM, XAvier Periole wrote:
The use of the original code is quite straightforward, the post
processing is a bit more confusing but quite accessible.
That would be a great topic for a wiki How-To.
We have been using this code (the one
in some cases.
Any help to resolve the problem would be greatly appreciated.
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...@rug.nl wrote:
Thanks for the answer. I'll check gmx4.5.7 and report back
We have noticed that g_genbox issue with MARTINI but have not new able to
understand where it actually comes from. It might be a bug or just a miss
communication of the vdw radius with genbox that appears only with large
spheres.
On Apr 29, 2013, at 19:50, alex.bjorling
genbox works best when the box size of the solute is defined as the same as of
the water one used to solvate it. So you can build a water box with the
dimensions you want and them use it.
You can build a water box by using genconf -nbox and use a script to cut to the
dimensions you need,
It is not clear what you are asking. Could you try to reformulate your
problem/question?
Did you read the Louhivuori-PNAS papers? There are lots of details in the
supplementary material.
On Apr 27, 2013, at 6:43, song.yongshun song.yongs...@163.com wrote:
Dear all:
I was using the MFFA
and the energy well conserved (400 ns of run). I do know if it is
optimal but it works for my system.
Stephane
--
Message: 1
Date: Fri, 26 Apr 2013 07:58:12 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx
Hi,
I have been recently using the REMD code in gmx-407 and gmx-453 and got a few
systems crashing for unclear reasons so far. The main tests I made are using
gmx407 but it is all reproducible with gmx453. The crashing was also reproduced
(not necessarily at the same time point) on several
Did you visualise the system? T in function of time? Epot in function of time?
As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist =
1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if
nstlist =10.
On Apr 25, 2013, at 1:10 PM, ABEL Stephane
visualized my system at the end of the NPT run, the na+, water,
surfactant, octane molecules form a slab with void
What's wrong ?
Stephane
--
Message: 5
Date: Thu, 25 Apr 2013 13:34:21 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx
or not they then crash) then there looks like
there may be a problem with the REMD implementation that is perhaps evident
only with the kind of large time step Martini takes?
Mark
On Thu, Apr 25, 2013 at 1:28 PM, XAvier Periole x.peri...@rug.nl wrote:
Hi,
I have been recently using
:52:09 +0200
From: XAvier Periole x.peri...@rug.nl
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl
Content-Type: text/plain; charset=windows-1252
Well ? 400 ps
I think your original problem is that you define only one charge group for the
entire molecule/polymer. You need to define each bead in a separate charge
group and things will be fine :)) you do not have charges anyways.
As far as I know angles have never made martini unstable but the
I have not followed the thread but concerning the solvation of a
protein using genbox you need to:
1- use a box of water that has the exact size of the final box you
want (you make it yourself using any tool you want) and you need to
define the box size of the protein file as the one of
Well either you use more replicas or you reduce the temperature
range ...
There is no way around!
On Nov 19, 2012, at 5:54 PM, Kenny Bravo Rodriguez wrote:
Dear All,
i am trying to performed REMD simulations using Gromacs.
My question is concerning the temperature distribution and the
From what I remember from my earlier impressions ... the equations
are not correct when the system is not neutral. In your case the
charge is significantly high ...
On Nov 2, 2012, at 9:36 AM, Felipe Pineda, PhD wrote:
Hi,
I recently sent a query, but it was probably not appealing
Martini FF cannot model changes in secondary structure ... other CG FF
can. You'll find them easily in the literature. Notably the ones from
Deserno or Derreumaux.
On Oct 10, 2012, at 2:03 PM, rama david wrote:
Hi friends,
I planed to use the martini force-field for my simulation study
Nope, but on other softwares.
On Oct 10, 2012, at 2:50 PM, rama david wrote:
Thank you for your reply,
Are these Cg can be used in Gromacs.
Thank you in advance.
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri...@rug.nl
wrote:
Martini
Periole x.peri...@rug.nl
Nope, but on other softwares.
On Oct 10, 2012, at 2:50 PM, rama david wrote:
Thank you for your reply,
Are these Cg can be used in Gromacs.
Thank you in advance.
With best wishes and regards,
Rama david
On Wed, Oct 10, 2012 at 6:13 PM, XAvier Periole x.peri
Well ... it always depends on what you want to do but the file on the
link you give are the official website and they should be reliable :))
On Oct 9, 2012, at 12:04 PM, rama david wrote:
Hi Gromacs friends,
I am interested in Martini force-field and application in lipid
bilayer.
I
You may want to try the forum on rte cgmartini.nl for more ...
In short:
try martinize.py -h it should give you options to separate the chain
topologies. If it does not work that means your chains are not defined
as two in the input.
Their is not direct manner to CG a lipid file ... the
-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
on behalf of XAvier Periole [x.peri...@rug.nl]
Sent: Wednesday, September 05, 2012 5:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] using martinize.py to martinize two chains
complex
You may want to try the forum on rte
There is no script generating an elastic network in Gromacs.
You could use the script that we developed in the context of the
Martini CG model (cgmartini.nl) but it would be certainly easier for
you to simply write a script that would rad the Clapha coordinates and
define the ones that
you give. So between Calpha the distance is about 0.38
nm ... if you use a dynamic bond description in VMD and select the
Calphas ... a cutoff of 4.0 would show you the connections.
Thanks,
Mohan
On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole x.peri...@rug.nl
wrote:
There is no script
rmsf is what you are looking for. g_rmsf should help.
On Jul 14, 2012, at 16:23, Igor Druz idruz...@gmail.com wrote:
Hello,
I would like to compare amplitude of motion of a specific atom in two
sets of MD simulations. Something like rms of displacements about the
equilibrium position
Thee are not yet parameters for DDM but indeed the parameters for both
the head and the tail are defined separately. It would be very useful
to combine them and start building a detergent parameter library ...
the topologies would have to be tested against experimental and/or
atomistic
Hi,
You do not need to use the polarizable martini water model to calculate the
dipole of molecules. Or I am missing a point here!
g_dipole should do the work
XAvier.
On May 13, 2012, at 15:11, dina dusti dinadu...@yahoo.com wrote:
Dear Justin,
Thank you very much from your response.
Interesting ...
do you have a reference for this?
XAvier.
On May 14, 2012, at 12:01 PM, Dommert Florian wrote:
On Mon, 2012-05-14 at 09:59 +0200, XAvier Periole wrote:
Hi,
You do not need to use the polarizable martini water model to
calculate the dipole of molecules. Or I am missing
The separation of groups for temperature control is originally
necessary to avoid (or correct for) temperature gradient in the
system, which occurs when systems parts have different frequencies of
motions. Typically the water molecules and a protein would be
separated to avoid the
Not sure but you could compare with unbiased histogram constructed
independently.
On Apr 23, 2012, at 11:55 AM, Gavin Melaugh wrote:
Hi all
Are the histograms from histo.xvg (output of g_wham) the biased or
unbiased distributions?
Cheers
Gavin
--
gmx-users mailing list
Where did you find the topology?
On Apr 10, 2012, at 10:44 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have doubt about definition of tiofen ring in MARTINI CG force
field. May I ask you to help me, Please?
I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C-
C. Is it
Try to use constrains = all-bonds which is the way to use Gromos force fields.
On Mar 26, 2012, at 12:30, SebastianWaltz
sebastian.wa...@physik.uni-freiburg.de wrote:
Dear Gromacs user,
I try to simulate the human Villin head peace HP35 in approx. 6000 water
molecules (spc) with the
Yes unfortunately the transformation is only inplemented in the version
available on the martini page.
On Mar 9, 2012, at 10:30, francesca vitalini francesca.vitalin...@gmail.com
wrote:
Either you develop your own version of the mapping or I guess you have
to use the old version...sorry,
Did you define the mapping in the atomistic topology?
On Mar 6, 2012, at 10:57, dina dusti dinadu...@yahoo.com wrote:
Dear Gromacs Specialists,
I have one problem about g_fg2cg. I want convert structure of butanole in fg
to cg by g_fg2cg, but I take this error:
Program g_fg2cg,
It was a good idea to ask! You might want to try the MARTINI forum at
the cgmartini.nl web site, though.
In short the way you did it will probably fill up the box with more
water or antifreeze particle than necessary ...
As an alternative you may want to simply replace 10% of the
and index.ndx files, is it
correct?
Best Regards
Sara
From: XAvier Periole x.peri...@rug.nl
To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Sent: Tuesday, December 13, 2011 5:34 PM
Subject: Re: [gmx-users] antifreeze particle in martini coarse
The website has been updated to fit a CG tutorial starting monday in
Lausanne.
The manner of the construction you describe in your email is not the
proper way to do it!
The new script is doing it properly.
If you want the old script to only generate the elastic network (as it
seems
by trial and error, just based on inter-bead
distances, but it would be nice to have it officially documented.
Mike
On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole x.peri...@rug.nl wrote:
it must be some example of mapping lipids on the website: cgmartini.nl
On Aug 30, 2011, at 3:55 AM
it must be some example of mapping lipids on the website: cgmartini.nl
On Aug 30, 2011, at 3:55 AM, Michael Daily wrote:
Hi all,
I am trying to reverse-map some martini lipids to united atom. In
order to do this, I'd prefer to have an EXACT definition of the aa-
to-cg mapping. I cannot
You may have wanted to have sent the message to the gmx list!
XAvier.
Begin forwarded message:
From: nicoletta liguori fisico...@gmail.com
Date: July 26, 2011 5:28:29 PM MDT (CA)
To: x.peri...@rug.nl
Subject: density error bars
Hi,
I'm using Gromacs and its tools to sample some kind of
One potential problem you have is that as Justin mentioned your minimum
is not well defined and certain much less well sampled than the long
distances
windows. Small peptides (depends the size) may sample relevant phase
space to get reasonable convergence within 8 ns when free in solution;
in
Well I do not know how g_wham is doing but it is likely that it does
align
different pmf obtained through the bootstraap the their minimum.
Justin just answered. The other alternative is to inverse your distances
with the data files.
On Jul 21, 2011, at 2:57 PM, Rebeca García Fandiño wrote:
Yes, include the harmonic restrain(s) directly into the topology. Then
you may
convert the info (distance(s), angle(s)) into the g_wham format
(which I do not
know but should be reasonably easy) or use another script to get your
PMF or
make you own ... it is possible.
On Jul 18, 2011,
this residence time in
gromacs, so I'm trying to find a trick that can give me a
pourcentage of the time of my simulation where a certain water
molecule stays in the specific area of my protein.
Regards,
Carla
On Tue, Jul 12, 2011 at 5:51 PM, XAvier Periole x.peri...@rug.nl
wrote:
Dear Boafu
Dear Boafu,
This sounds like a great tool!
Carla, note that once you've ordered the water molecules you loose
the continuity of their trajectories ... that is because you order
them in
function of their distance to the protein.
I am not sure the definition you give will give you the answer
Well, there must be some thing some where that you did the wrong way :))
You should try again from the start and may be try to post on the
Martini website forum
www.cgmartini.nl
XAvier
On Jun 20, 2011, at 9:41 AM, Naba wrote:
Dear Users/Developers
I am trying to set a coarse-grained MD
You should a have good read at the original papers. They are mentioned on the
web site. They will answer all your questions.
On May 28, 2011, at 6:03, Chih-Ying Lin chihying2...@gmail.com wrote:
Hi
I want to get the rotational axis about the protein domain motion.
From the DynDom
Two things you have to be careful about:
1- use trr trajectory files. xtc precision is not sufficient and it
will give a lot of discrepancies at least for the bonded terms.
2- set the nstlist to 1 as the neiboring list should be undated for
each frame and not every 5/10 as it is normally set
reference:
Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M (1995) J.
Comput. Chem. 16, 273-284.
On May 11, 2011, at 2:34 PM, Laura Leay wrote:
Can anyone explain in detail the method that gromacs uses to calculate
surface area? Which surface area is it calculating (e.g., connolley,
On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote:
Hi All
I have generated several PMF curves for the one system using umbrella
sampling. In the first part of the curve (barrier region) I use a high
force constant with small intervals between the windows. The latter
part
of the curve I use
. With respect to your answer of my first query.
What if you had two windows practically on top of each other, but one
was not supposed to be there. e.g A window with r0 of 0.80 nm and
centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm.
Gavin
XAvier Periole wrote:
On Mar 31, 2011
around 0.80 nm should work.
-Justin
Gavin
XAvier Periole wrote:
You can present the data differently:
you have two windows at 0.78 nm giving different distribution.
That indicates these windows are not converged. Does not mean
that the others (0.80 nm) are converged :))
On Mar 31, 2011, at 12:20
You can use any GROMACS version to run a simulation
with the Martini Force field. IT is only if you want to back-map
your system to an atomistic resolution that you'll have to
use the gmx331 modified version.
On Mar 27, 2011, at 8:25 PM, Edroaldo Lummertz da Rocha wrote:
Dear GROMACS users,
It is unfortunately often that cations on their binding sites in proteins are
not stable. Either the site reorganize or the ion leaves.
The problem is that ions parameters and especially double charged ones are
difficult to parameterize.
It is often that people use additional restrains
Hi Jesper,
This occurs when you ask for a number of steps that exceed the
the size of an integer! I got the same problem recently ...
The only solution I found was to make a new mdp file where t0
is the old time and asking for the extension you need ... you can
give trr and edr files to grompp
,
Tsjerk
2011/2/24 Jesper Sørensen li...@jsx.dk:
Hi Xavier,
That worked, thanks… Would it also work if I just gave the old
state.cpt
file to mdrun?
Jesper
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org
]
On Behalf Of XAvier Periole
Sent: 24. februar 2011 12:19
. Note also that the conformations sampled at high
temperature with position restrains on the lipids to avoid deformation
will be difficult to interpret!
Cheers
Jianguo
From: XAvier Periole x.peri...@rug.nl
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, 22 February
A few notes:
- the original method (Kumar-JCC-1992) that inspired wham was actually
developed to mix different temperature simulations. It is however not
clear
for the type of system you are simulating how much a 500K simulation
would be useful to improve the sampling at 300 K or so. The
You have to make sure of two things:
1- use a reference (gro or tpr) where the molecule is whole! The tpr is
prefered since the molecules are defined.
2- with such a reference and the option -mol you'll get a trajectory with the
protein as a whole.
On that trajectory you may apply more
(Evelyne Deplazes)
4. Re: removing pbc jumps from trajectory (XAvier Periole)
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Mon, 21 Feb 2011 08:14:26 +0100
Subject: Re: [gmx-users] g_covar
g_dist
On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:
Dear Gromacs Users,
I would like to know if there is in gromacs an option how to
calculate how many contacts has a certain atom i(n a molecules of
interest) with water during the whole MD simulations (or at each
step of MD).
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning is of primary importance.
2- you want to simulate unfolded protein ... indeed
On Feb 14, 2011, at 7:24 PM, devicerandom wrote:
On 14/02/11 13:42, XAvier Periole wrote:
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short
:))
have look there cgmartini.nl
Regina
Quoting XAvier Periole x.peri...@rug.nl:
Dear Regina,
You have two problems:
1- the parameterization of phosphorylated serine should be done
following the same philosophy of Martini. Check the Martini papers
to see how this is done. In short partitioning
On Feb 10, 2011, at 3:08 PM, jk...@ifr88.cnrs-mrs.fr wrote:
Hi,
I'm running an Umbrella Sampling analysis, with 1A steps in the
reaction coordinate (distance) to estimate a PMF. However, owing to
(high?) energetic barriers between my two proteins, some coordinates
are not sampled. I
On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:
Dear all
I have generated a PMF curve for introducing a guest molecule into a
host molecule using the umbrella sampling method. The curve seems
fine,
but there are no overlaps between histograms in the barrier region. To
circumvent this I
sampled ... that might result
in a
funny and wrong profile. You might want to look at your simulations for
funny things ...
Gavin
XAvier Periole wrote:
On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote:
Dear all
I have generated a PMF curve for introducing a guest molecule into a
host
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