Charges... Hmmm...
I think you have incorrect data types passed to x2top.
Vitaly
>
> I think the result cannot be trusted because the total charge is 1.2, which
> seems impossible. I just used the result calculated by Material Studio and I
> used the value of charge on the internal atoms. The at
Dear all,
I have performed a MD of a polymer chain interacting on a carbon nanotube
using gromacs 4.0.7. I need to evaluate the potential energy of the polymer
alone, during the dynamic, so to compare with its potential energy in vacuo.
During the dynamic, the CNT was frozen, and I used exclusions
On 24/03/2010 7:34 PM, Andrea Minoia wrote:
Dear all,
I have performed a MD of a polymer chain interacting on a carbon
nanotube using gromacs 4.0.7. I need to evaluate the potential energy of
the polymer alone, during the dynamic, so to compare with its potential
energy in vacuo. During the dynam
Mark,
thank you for the fast reply. My original mdp, the one I used to run the
dynamics is
nstcgsteep = 1000
nbfgscorr= 10
emstep = 0.02
emtol= 10
dt = 0.002
nsteps = 1500
comm-mode
Hi Sukesh,
Great. This makes things much clearer. So basically what you'd need to
do is to divide each i,j-th element of the covariance matrix you
obtained (covar.dat) by the sqrt of the ii-th and jj-th diagonal
element. That will commonly turn a covariance matrix into a
correlation matrix. But,
I'm not sure if this helps, but have you tried link/ dummy atoms like
you use them for QMMM? For dummies add a line to ff***nb.itp where you
define them to have neither charge nor weight (also 0 for LJ-pot).
Then add them to your topology-file. Check out
http://www.gromacs.org/Documentation
I found something:
apparently, I need to remove the energygrp_excl = CNT CNT from the original
mdp, generate a new tpr with this modified mdp and grompp, and then use
tpbconv to create the simulation file for the subsystem.
my energy groups are still CNT and pcl and now g_energy gives something l
Hello,
I have protein in my protein, for which i want to run MD simulation.
Could you please help me to know how to generate topology file for Manganese
and which force field to use, as none of the force field in Gromacs supports Mn
ion.
Please Help
Regards
--
Sonali Dhindwal
The INTER
Hello,
I have a Manganese ion in my protein, for which i want to run MD simulation.
Could
you please help me to know how to generate topology file for Manganese
and which force field to use, as none of the force field in Gromacs
supports Mn ion.
Please Help
Regards
--
Sonali Dhindwal
--- On Wed,
sonali dhindwal wrote:
Hello,
I have protein in my protein, for which i want to run MD simulation.
Could you please help me to know how to generate topology file for
Manganese and which force field to use, as none of the force field in
Gromacs supports Mn ion.
Parameterization is considere
Thanks for your help
I hope it will work.
Regards
--
Sonali Dhindwal
--- On Wed, 24/3/10, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein
To: "Discussion list for GROMACS users"
Date: Wednesday, 24 March, 2010, 5:44 P
On 24/03/2010 11:37 PM, sonali dhindwal wrote:
Thanks for your help
I hope it will work.
Better than just hoping is design a small test case to see if the
parameters are vaguely suitable for *your* purpose - and read up on how
they were parameterized and for what purpose... Your problem could
Dear gromacs users:
How to reconstruct potentials of mean force through time series analysis of SMD
or pulling simulations; for example, software or script using, how to
reconstruct PMF in detail?
thank you very much!
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.g
xi zhao wrote:
Dear gromacs users:
How to reconstruct potentials of mean force through time series analysis
of SMD or pulling simulations; for example, software or script using,
how to reconstruct PMF in detail?
thank you very much!
http://www.gromacs.org/Documentation/Tutorials#Umbrella
Dear sir :
I want to analye a collective motions of a single structure by PCA , for
example, how to choose reference structure using g_covar; how to show its
position in 2D-projection (conformational space)?
thank you very much!
--
gmx-users mailing listgmx-users@gromacs.org
http://l
xi zhao wrote:
Dear sir :
I want to analye a collective motions of a single structure by PCA , for
example, how to choose reference structure using g_covar; how to show
its position in 2D-projection (conformational space)?
thank you very much!
There have been several discussions on this to
dear Mr Justin A. Lemkul :
I have read your tutorial ,it is suitable for umbrella sampling method, it is
not for SMD, wham or g_wham can not be used!
Thnak you!
--- 10年3月24日，周三, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] how to reconstruct potentials of mean force throu
xi zhao wrote:
dear Mr Justin A. Lemkul :
I have read your _tutorial ,it is suitable for umbrella sampling method,
it is not for SMD, wham or g_wham can not be used!_
_Thnak you!_
If you want to use SMD trajectories to calculate free energy changes, you will
need Jarzynski's inequality an
Hi,
Now that particular reference was not a very suitable one for this question :)
The proper reply here is:
There are no collective motions in a single structure, period!
Do some background reading on PCA, and some more on PCA as applied to
MD simulations. There is some information in the manua
Dear Mr Justin A. Lemkul :
Thank you for your advice, can you give more suggetions?
Thank you very much!
--- 10年3月24日，周三, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题: Re: [gmx-users] how to reconstruct potentials of mean force through time
series analysis of SMD or pulling simulation
Dear Mr Justin A. Lemkul :
In fact, please read the document
http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf,
the document shows the PMF can be reconstructed from the SMD, why?
thank you!
--- 10年3月24日，周三, Justin A. Lemkul 写道：
发件人: Justin A. Lemkul
主题
xi zhao wrote:
Dear Mr Justin A. Lemkul :
Thank you for your advice, can you give more suggetions?
Thank you very much!
Not really. If you search "Jarzynski" in the mailing list archives, you get 8
results, indicating to me that this is not a particularly popular way to
calculate free
xi zhao wrote:
Dear Mr Justin A. Lemkul :
In fact, please read the document
http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-513/paper06.pdf,
the document shows the PMF can be reconstructed from the SMD, why?
I never disputed that fact. Please the post I just sent you.
Ah, I can make some advertisement for my own work again.
If you can do equilibrium simulations these will always be more efficient
than non-equilibrium, as Justin also pointed out below.
I have published a case where you can not (or not efficiently) do equilibrium
simulations, because you don't kn
Hi,
I want to test different values of cutoff for vdw. However, in the list someone
said cutoff = 0.9 for vdw was used for paramaterizing of Gromos force field,
other values would cause error, and also there was someone saying that cutoff
for vdw should be set to 1.4. Can someone make this que
Qian Wang wrote:
Hi,
I want to test different values of cutoff for vdw. However, in the list
someone said cutoff = 0.9 for vdw was used for paramaterizing of Gromos
force field, other values would cause error, and also there was someone
saying that cutoff for vdw should be set to 1.4. Can
>
> Stefan Hoorman wrote:
> >
> >
> > Stefan Hoorman wrote:
> > >
> > > Stefan Hoorman wrote:
> > > > I have tried using g_bundle in order to analyse helix axes
> > in my
> > > > transmembran helices. I created two groups in my ndx file
> that
> > >
Stefan Hoorman wrote:
I have tried using g_sgangle, but the problem is that it does not
calculate the principal axis of the helix. Since g_sgangle allows me to
choose at maximum 3 atoms per analysis, it is quite difficult to perform
such an analysis if one is to do this for 4 or five diffe
Hello all,
I have a simulation running for a hydrate (with CO2) and water in contact
with each other. I run the simulation at 280K at which the hydrate melts and
finally the system is just liquid water with CO2 in it. However, as the
simulation proceeds the box begins to expand in the z-direction
> Hi,
>
> I want to test different values of cutoff for vdw. However, in the list
> someone said cutoff = 0.9 for vdw was used for paramaterizing of >Gromos
> force field, other values would cause error, and also there was someone
> saying that cutoff for vdw should be set to 1.4. Can >someone m
>
> Stefan Hoorman wrote:
>
>
>
> > I have tried using g_sgangle, but the problem is that it does not
> > calculate the principal axis of the helix. Since g_sgangle allows me to
> > choose at maximum 3 atoms per analysis, it is quite difficult to perform
> > such an analysis if one is to do this f
Stefan Hoorman wrote:
Stefan Hoorman wrote:
> I have tried using g_sgangle, but the problem is that it does not
> calculate the principal axis of the helix. Since g_sgangle allows
me to
> choose at maximum 3 atoms per analysis, it is quite difficult to
perfor
On Mar 24, 2010, at 10:58 PM, Vitaly V. Chaban wrote:
Hi,
I want to test different values of cutoff for vdw. However, in the
list someone said cutoff = 0.9 for vdw was used for paramaterizing
of >Gromos force field, other values would cause error, and also
there was someone saying that c
Hi
I want to do Coarse-Grained simulation in Gromacs. I have one CG force
formula, which I plan to implement by adding a short code in do_force()
routine in Gromacs 4.0.7 source code.
After browsing through the do_force() code, I am now familiar with data
structure relevant to add the new force.
On 25/03/2010 2:42 PM, Sikandar Mashayak wrote:
Hi
I want to do Coarse-Grained simulation in Gromacs. I have one CG force
formula, which I plan to implement by adding a short code in do_force()
routine in Gromacs 4.0.7 source code.
After browsing through the do_force() code, I am now familiar w
Hi ALL,
Is there any way in GROMACS to get the residue list (acceptor-donor list)
for an entire simulation? Using g_hbond we get the number of h-bonds at
every frames. But I want to get the list of residue pairs forming those
hbonds at every frame. Any suggestion is welcome.
Thanks a lot in advanc
well if I need to add it by myself, I am not very sure in what variable to
add it to. Like I said, I know to add the force on the atom i do
f[indxofatom][XX]= forcevalue, where to potential value due to this force?
thanks
sikandar
On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham wrote:
> On 25/03/
- Original Message -
From: Sikandar Mashayak
Date: Thursday, March 25, 2010 15:12
Subject: Re: [gmx-users] CG Force and Potential through do_force()
To: Discussion list for GROMACS users
> well if I need to add it by myself, I am not very sure in what variable to
> add it to. Like I s
- Original Message -
From: Anirban Ghosh
Date: Thursday, March 25, 2010 15:10
Subject: [gmx-users] Hydrogen Bond Acceptor-Donor List
To: Discussion list for GROMACS users
> Hi ALL,
>
> Is there any way in GROMACS to get the residue list (acceptor-donor list) for
> an entire simulation?
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