Including Fe2+ should not be very difficult, look at the definitions for Cu2+
or others in ffG53a6.nb or any other forcefield you want to use. You need to
find the correct Lennard-Jones parameters C6 and C12 and then validate your
model.
I am not sure, what the FES molecule is, but developing a
Hi Vinod,
How did you build your top file for input to grompp ? genconf would have given
you a multiplied system in .gro structure format. I think you should generate
.top file from this .gro file using pdb2gmx and then use that as grompp input.
Regards,
Nikhil
_
Thanks for reply ,The problem is solved .The problem was with topology file
.
On Fri, Jun 4, 2010 at 4:44 PM, Justin A. Lemkul wrote:
>
>
> jani vinod wrote:
>
>> Hello,
>> I build a system solvated in water .
>> Then replicated the system using genconf. Now when I am running grompp i
>> am
>> g
Hi all,
I want to get the forces out of the .trr file using the
template.c given. My question is what flag should I use in
the last loop to get the force f? I don't find anything in
the directory which is given in the example.
Thanks
--
gmx-users mailing listgmx-users@gromacs.org
http://lis
Hello Chris, thanks for the tips, they were very helpful.
Now a new problem appeared. I'm trying to separate the
two benzene molecules from one another while maintaining
the displacement vector aligned with the z axis. For that I
have used "pull_geometry = direction". However, at the end of the
sim
Hi ,Happy world environment day! This is our only home and look what we are doing to it.
Years of neglecting nature - our most precious resource - has caused damage all around the world, and it will only get worse if the exploitation continues.
There is a movement lead by organizations like Gr
Dear GMX users,
I don't know why I can't open the tutorial of free energy calculations on this
website http://www.gromacs.org/Documentation/Tutorials. Can you open it? Thanks
very much!
All the best,
fancy--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinf
I agree the code is fine. Is there a parameter that I need to change
to increase the tolerance? I have issues energy minimizing a small
molecule in the presence of a macromolecule. One work around is to
increase the energy of the small molecule, so that the macromolecule
no longer domina
Hello,
I have 125 hexane molecules in a box of 0.25nm3. The desnity I calculate
from this number of molecules is approx. 71000 Kg/m3. To make sure that the
density remains constant I am doing NPT simulation. From this simulation I
see the density is 577 Kg/m3. and the volume is 30 nm3. Please guid
Morteza Khabiri wrote:
Dear users
I have a dimer protein in the water box. It was run for 30ns.
during the simulation dimer split to two monomer. This things happen bc of
PBC. ( I checked it by vmd pbc option )
to have a two monomer together during trajectories (for visualization)
I have
Dear all:
After I read the paper, "Picosecond Melting of Ice by an Infrared Laser
Pulse: A Simulation Study" (Carl Caleman and David van der Spoel, Angew.
Chem. Int. Ed., 2008, 47, 1417-1420), I decided to implement a
time-dependent electric field on my simulation system. But when I read the
groma
Hi Arthur,
The most useful option from my experience is to run Gromacs in double
precision.
You also can try to make emstep smaller (after an initial minimisation
of the crude structure) and use l-bfgs.
Good luck,
Ran
--
--
Ran Friedman
Postdo
- Original Message -
From: Sebastian Waltz
Date: Tuesday, June 8, 2010 18:48
Subject: [gmx-users] which flag for the force
To: gmx-users@gromacs.org
> Hi all,
>
> I want to get the forces out of the .trr file using the
> template.c given. My question is what flag should I use in
> the la
Hi,
I would like to add an external force f(x) on some atoms during the
simulation, where x is the Cartesian coordinates of these atoms.
Each component of the force can only be calculated with the whole set of
coordinates, i.e., (f1, f2, ..., fn) = f(x1, x2, ..., xn)
Is there a possible way
- Original Message -
From: Ting Zhou
Date: Tuesday, June 8, 2010 19:13
Subject: [gmx-users] add external force
To: gmx-users@gromacs.org
> Hi,
>
> I would like to add an external force f(x) on some atoms during
> the simulation, where x is the Cartesian coordinates of these atoms.
>
On 06/08/2010 11:18 AM, Mark Abraham wrote:
- Original Message -
From: Ting Zhou
Date: Tuesday, June 8, 2010 19:13
Subject: [gmx-users] add external force
To: gmx-users@gromacs.org
> Hi,
>
> I would like to add an external force f(x) on some atoms during
> the simulation, where x
Hi gromacs users
I want to simulate pr-dna by gromacs.I read a article (Biophysical Journal
87(6) 3799–3813) inwhich helical parameters for DNA (rise, slide, twist,
roll, tilt, shift) calculated by md simulation, but I did not understand two
things:
How and what command these parameters were cal
Hi,
For one thing; to keep density constant (as in fixed) you want NVT, not
NPT. NPT could, depending on your starting state, allow for initial
drift in the system size.
Cheers,
Erik Marklund
Moeed skrev:
Hello,
I have 125 hexane molecules in a box of 0.25nm3. The desnity I
calculate fro
shahab shariati wrote:
Hi gromacs users
I want to simulate pr-dna by gromacs.I read a article (Biophysical
Journal 87(6) 3799–3813) inwhich helical parameters for DNA (rise,
slide, twist, roll, tilt, shift) calculated by md simulation, but I did
not understand two things:
How and what co
Dear Eudes:
You can make my job a whole lot easier! First, please go back through
all of the comments that I gave you last time and reply to them one by
one. Did you do them? What did you see? Second, please include your
new .mdp and some quantitative results to better explain what you see
Dear Gromacs users,
I am doing thermodynamic integration in order to compute the change in free
energy upon increasing the electric charges of a water molecule from zero
(lambda=0) to its actual partial charges (lambda=1). I get significantly
different results of with Gromacs 3.3.1 on one hand a
Hello,
you can use for example Curves (Nucleic Acids Research, 2009, Vol. 37, No.
17 5917-5929) or 3DNA
(http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html) to calculate them
from any trajectory, I did but never used gromacs for this, I don't know
if it is possible.
Hope this helps,
Best
Attilio
schn...@uni-heidelberg.de wrote:
Dear Gromacs users,
I am doing thermodynamic integration in order to compute the change in free
energy upon increasing the electric charges of a water molecule from zero
(lambda=0) to its actual partial charges (lambda=1). I get significantly
different results
- Original Message -
From: Ting Zhou
Date: Tuesday, June 8, 2010 19:26
Subject: Re: [gmx-users] add external force
To: Discussion list for GROMACS users
> On 06/08/2010 11:18 AM, Mark Abraham wrote:
> >
> >
> >- Original Message -
> >From: Ting Zhou
> >Date: Tuesday, June 8, 2
Hi all:
I am trying to simulate a polysaccharide in solution of water and CsCl, but
cesium is not parametrized in the gromacs 4. I am using the force
field GROMOS 96.
I have looked for the parameters of Cs+ in the OPLS Force field and I have
created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Al
Cecilia Fernándz Gauna wrote:
Hi all:
I am trying to simulate a polysaccharide in solution of water and CsCl,
but cesium is not parametrized in the gromacs 4. I am using the force
field GROMOS 96.
I have looked for the parameters of Cs+ in the OPLS Force field and I
have created 4 files: Cs.
Dear Chris, I'm so sorry for surperficial email.
You are correct because in the previous message
I forgot to mention that now the simulation was
performed in water (naturally with PBC).
The main parameters of the simulation are given below.
As I said, I wish to keep the displacement of the pulled m
Hi,
I am running a very short md run for 100 steps and I get the Infinite giga
flopses error. I stored info at every step to check if the simulation is
running. And the log file has all the variables for each time-step with
reasonable values. I don't understand the meaning of the message at the e
Sai Pooja wrote:
Hi,
I am running a very short md run for 100 steps and I get the Infinite
giga flopses error. I stored info at every step to check if the
simulation is running. And the log file has all the variables for each
time-step with reasonable values. I don't understand the meaning
> Hi all:
> I am trying to simulate a polysaccharide in solution of water and CsCl, but
> cesium is not parametrized in the gromacs 4. I am using the force
> field GROMOS 96.
> I have looked for the parameters of Cs+ in the OPLS Force field and I have
> created 4 files: Cs.atp, Cs.itp, Csnb.itp and
Hello,
I am trying to simulate a DPPC bilayer, 180 lipids total, ~13000 TIP3
and 50 K, 50 Cl counter-ions. The standard charmm27r DPPC parameters
have very large charge groups, so I went through them and made them
smaller (4 atoms each, on average), following the comments from
grompp. I have tried
Hello gmx users !!
I was trying to use template.c. There I printed out the coordinates of a
trajectory file using the printf statement as under:
printf("Coordinates at t=%8.3f : %8.5f %8.5f
%8.5f\n",fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]);
The output was
Reading frame 100 time 4400.000
Chandan Choudhury wrote:
Hello gmx users !!
I was trying to use template.c. There I printed out the coordinates of a
trajectory file using the printf statement as under:
printf("Coordinates at t=%8.3f : %8.5f %8.5f
%8.5f\n",fr.time,fr.x[n][XX],fr.x[n][YY],fr.x[n][ZZ]);
The output was
Re
Chandan -
Hmm... What's the problem? template.c gives the numbers in NANOMETERS
while PDB file contains them in ANGSTROMS.
To my knowledge, nowadays gromacs people use XDRFILE library to work
with trajectories -
http://www.gromacs.org/index.php?title=Download_%26_Installation
--
Dr. Vitaly Chab
Dear Mark,
When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any
problem. So I guess it's related to the assembly loops for BG.
Thanks,
Lanyuan
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Sat, 5 Jun 2010 03:31:33 +1000
Subject: Re: [gmx-users] PME probl
Dear Eudes:
This is better, but I'm afraid that I'm going to have to insist on
getting everything I asked for. Please see my previous message.
Chris.
-- original message --
Dear Chris, I'm so sorry for surperficial email.
You are correct because in the previous message
I forgot to mention t
Hello Chris, thanks for the reply. Below his message commented walkthrough.
In your email you asked me for quantitative results. All I have so far is
a visual inspection of the pulling trajectory. All I can see are
the two molecules moving linearly away from each other in a rectangular box
of dimen
HI
Its not working for me either.
But for free energy tutorials using GROMACS, I think the one written by Prof
Mobley is like Bible.
The link is as follows:
http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial
But the one written by Prof Alan Mark (who is now in Queensland Univ
Thanks Justin. I think you are right. I always encounter this problem with
extremely small runs.
On Tue, Jun 8, 2010 at 11:04 AM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> I am running a very short md run for 100 steps and I get the Infinite giga
>> flopses error. I stored in
Hi Fancy,
The following link shows the change from p-cresol to Toluene. So follow
the steps in the same by converting threonine to methionine.
http://compbio.chemistry.uq.edu.au/education/Free-Energy_Course/0.introduction.html
Regards
Sai
2010/6/5 fancy2012
> Dear GMX users,
>
> I want to c
Dear Gromacs users,
it seems what I have stumbled upon is a known bug of Version 3.3.1.
Here are the corresponding discussions:
http://bugzilla.gromacs.org/show_bug.cgi?id=175
http://www.mail-archive.com/gmx-users@gromacs.org/msg12180.html
Best
Emanuel
--
gmx-users mailing listgmx-users@g
- Original Message -
From: LuLanyuan
Date: Wednesday, June 9, 2010 2:10
Subject: RE: [gmx-users] PME problem on BG/P cluster
To: gmx-users@gromacs.org
---
|
> Dear Mark,
> When I set NOASSEMBLYLOOPS to 1, the simulation could
Hi,
I have trouble searching mailing lists so I apologize if this has already
been answered in some query.
If sigma=epsilon=mass=1 is specified in .top file then for specifying T*=1
in the Thermostat does one need to set ref_t ~ 120 ?
Similarly, to specify ref_p for the Barostat, is there a sim
- Original Message -
From: Sai Pooja
Date: Wednesday, June 9, 2010 8:07
Subject: [gmx-users] Reduced LJ Units
To: Discussion list for GROMACS users
> Hi,
> I have trouble searching mailing lists so I apologize if this has already
> been answered in some query.>
> If sigma=epsilon=mass=
Thanks, Mark. I've post it on the bugzilla. I'm glad to try the new assembly
loops on BG/P as well.
Lanyuan
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Date: Wed, 9 Jun 2010 07:48:26 +1000
Subject: Re: RE: [gmx-users] PME problem on BG/P cluster
- Original Message -
From: Lu
Thanks Mark. I looked at the link you has sent. However, with pressure
coupling I haven't seen such fluctuations for my system. The pressure value
is the one obtained at the end of a long NPT simulation - 10^8 steps with
dt=10^-4. The rms fluctuations in pressure are small, of the order of 1-0.1
b
Hi Morteza,
I had this problem when I was running a trimeric protein attached to an
oligosaccharide.
*I have used the following command:*
* *
*trjconv -s .tpr -f .xtc -o -boxcenter tric -pbc mol*
* *
*but it is not working.*
Do the following. It worked for me.
In the first round, run
Hello Justin,
I am trying to generate the top file for polyethylene chain using the
information from the archive:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html. In the
former post you said parameters in the I am referring to are not necessarily
correct.
1- By parameters you
Dear Eudes:
Thanks for working with me on this one! What you are getting is
actually what you are asking for in your .mdp file. You restrain the
Z-projection of the displacement, but do not affect the X and Y
components of the displacement with pull_dim = N N Y. If you want to
pull with s
Moeed wrote:
Hello Justin,
I am trying to generate the top file for polyethylene chain using the
information from the archive:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html. In
the former post you said parameters in the I am referring to are not
necessarily correct.
Hi All,
I am trying to simulate kinase domain (chain A) in complex with cyclin (chain
B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need
to keep only kinase domain flexible but cyclin fixed.
i put POSRES_B in define variable and tried to simulated the entire solvate
First, sorry for the revival of this thread so late (maybe it should be better
to start a new one).
> - Original Message -
> From: Dmitri Dubov
> Date: Thursday, May 27, 2010 19:11
> Subject: Re[2]: [gmx-users] Non-conservation of total energy while
> using structure file to resume the s
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