Hi
I want to add water molecule in my structure. Do anyone have idea how to
add water molecules in protein structure. I little aware of python.
How the gromacs spc216 add the water molecule. Can i get the code for the
same?
pooja
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On Mon, Aug 12, 2013 at 4:09 PM, wrote:
> Hi
>
> I want to add water molecule in my structure. Do anyone have idea how to
> add water molecules in protein structure. I little aware of python.
> How t
Thanks
I am looking for code (python, C++), not gromacs command line.
pooja
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
>
>
> On Mon, Aug 12, 2013 at 4:09 PM, wrote:
>
>> Hi
>>
>> I want to add water molecule in my structure. Do anyone have
Via an index file, I would guess... Or what do you mean exactly?
Dr. Vitaly V. Chaban
On Mon, Aug 12, 2013 at 5:26 AM, Kieu Thu Nguyen wrote:
> Dear users,
>
> I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
> i do not know how to choose the reference atom per lipid
Hi Pooja,
Do you mean solvating around the protein, or placing water inside? If you
feel brave, you can check out the C code of genbox. Genbox copies a box of
solvent to cover the box with the protein, and then removes all solvent
which has overlaps with the protein.
Cheers,
Tsjerk
On Mon, Aug
On 8/11/13 11:26 PM, Kieu Thu Nguyen wrote:
Dear users,
I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
i do not know how to choose the reference atom per lipid for an any type of
lipid, such as POPC, DOPC,...
Where i can get these references ?
Most people choose
Thanks so much ! I guessed should i choose it but i am not sure :-)
So, if most people choose it, i think it is ok.
On Mon, Aug 12, 2013 at 4:25 PM, Justin Lemkul wrote:
>
>
> On 8/11/13 11:26 PM, Kieu Thu Nguyen wrote:
>
>> Dear users,
>>
>> I want to use g_msd to measure diffusion coefficient
Re-sending to list; original bounced when we had some issues with
gmx-users over the weekend.
Mark
-- Forwarded message --
From: Mark Abraham
Date: Sat, Aug 10, 2013 at 11:49 AM
Subject: Re: [gmx-users] Assistance needed running gromacs 4.6.3 on Blue Gene/P
To: prentice.bis...@ru
Hi,
I think g_wham cannot symmetrize around a non-zero point. You'll have to
write a little awk script or so and this yourself. Or edit the g_wham code.
-zprof0 is not what you need. It sets the PMF to zero at a reference
point, where the free energy is defined to zero.
Best,
Jochen
Am 8/10/13
Hi Magnus,
I just read your mail. Sound very much like a bug, which never occurred
to me though. But I did not use -bs-method traj-gauss a lot. Does the
error also occur with -bs-method traj?
Btw: with -bs-method traj-gauss or traj, you need realistic estimates of
the autocorrelation times (ACTs)
Hi Jochen,
Seems as if this error was associated with the mpi version. Everything worked
ok when running it locally.
Best regards /
Magnus
On Aug 12, 2013, at 1:50 PM, Jochen Hub wrote:
> Hi Magnus,
>
> I just read your mail. Sound very much like a bug, which never occurred
> to me though.
Dear Gromacs users,
We would like to know which is the Force Field which is customarily
preferred for simulations of peptides and proteins.
Thank you very much.
Best regards,
Maria
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* Please s
It depends on what properties of peptides and proteins that you want to
explore.
~Thu
On Mon, Aug 12, 2013 at 7:19 PM, Maria Astón Serrano <
m.aston.serr...@gmail.com> wrote:
> Dear Gromacs users,
>
> We would like to know which is the Force Field which is customarily
> preferred for simulation
I like CHARMM.
Dr. Vitaly V. Chaban
On Mon, Aug 12, 2013 at 2:19 PM, Maria Astón Serrano <
m.aston.serr...@gmail.com> wrote:
> Dear Gromacs users,
>
> We would like to know which is the Force Field which is customarily
> preferred for simulations of peptides and proteins.
>
> Thank you very muc
On 8/12/13 8:19 AM, Maria Astón Serrano wrote:
Dear Gromacs users,
We would like to know which is the Force Field which is customarily
preferred for simulations of peptides and proteins.
Interestingly, this same question was just asked on the development list,
although the discussion indee
On this note, I wanted to ask about simulated unfolding of proteins. I have
a primarily alpha-helical-protein ( about 300 amino acids, 5 alpha helices,
no beta strands) and 3 of its single point mutants. Now, to answer the
question of relative stability, I want to place them in a water bath and
hea
thanks. One more question, is there an easy way to ask gromacs to output the
forces and the 2nd derivative? Or one has to modify the source code to do this?
Best,
JT
From: David van der Spoel
To: gmx-users@gromacs.org
Sent: Sunday, August 11, 2013 12:17 PM
Hi all,
I found one paper talking about they "implement a wall potential in the
pull module of the mdrun program". Does anybody know how they do it please? Is
it the similar method introduced in "User-specified potential functions" by
using following in mdp:
rilst = 1.0
coulombtype =user
On 8/12/13 12:52 PM, Li, Hualin wrote:
Hi all,
I found one paper talking about they "implement a wall potential in the pull module of
the mdrun program". Does anybody know how they do it please? Is it the similar method
introduced in "User-specified potential functions" by using followi
Hi Justin,
Thank you for your reply. I also suspect that they may use like " change
pull source code -->recomplie GROMACS -->run modified mdrun ". Do you know
where the source code of the pull code is located please?
Thanks,
--H L
From: gmx-users-bo
On 8/12/13 1:29 PM, Li, Hualin wrote:
Hi Justin,
Thank you for your reply. I also suspect that they may use like " change pull source
code -->recomplie GROMACS -->run modified mdrun ". Do you know where the source code
of the pull code is located please?
It's in src/mdlib - pull.c an
Hi Justin,
Thanks a lot. I found them. Other than changing the source code, is it
possible to write a script-like code to run with mdrun in order to apply this
wall potential please?
Thanks,
--H L
From: gmx-users-boun...@gromacs.org [gmx-users-boun...
On 8/12/13 2:13 PM, Li, Hualin wrote:
Hi Justin,
Thanks a lot. I found them. Other than changing the source code, is it
possible to write a script-like code to run with mdrun in order to apply this
wall potential please?
Doubtful. Again, I would try to get in contact with the authors
Dear all,
I am using your script charmm2gromacs for the conversion and I am facing
certain difficulties in the same.
My doubts are:
1. In NAMD is was using CHARMM36 parameters as the parameters dor DOPC
(dioleyl phopshotidyl choline). were available in only in that.
2. For cholesteryl es
Dear all ,
With reference to the thread on converting charmm36 lipid parameters to gromacs:
http://lists.gromacs.org/pipermail/gmx-users/2010-October/054515.html
The link mentioned :http://www.dbb.su.se/User:Bjelkmar/Ffcharmm no longer
works.
It says page not found. Kindly suggest me how to con
Dear all,
The thread on perl,scripts for converting charmm to gromacs states that the
package is deprecated and emailed off-list.
http://lists.gromacs.org/pipermail/gmx-users/2010-February/048506.html
How could I convert charmm to gromacs otherwise? Could anyone help me with
their scripts in t
On 2013-08-12 21:33, Revthi Sanker wrote:
Dear all,
The thread on perl,scripts for converting charmm to gromacs states that the
package is deprecated and emailed off-list.
http://lists.gromacs.org/pipermail/gmx-users/2010-February/048506.html
How could I convert charmm to gromacs otherwise? C
Hi,
I am trying to use do_dssp to generate a secondary structure map over time for
a 10-ns simulation. I have installed dssp_2.2.0 at the usual /usr/local/bin
I tried running it with the following command line
do_dssp -f md.xtc -s md.tpr -o ss.xpm -sc ss.xvg -dt 100 -tu ps; but ended up
with the
On 8/12/13 4:29 PM, Dipankar Roy wrote:
Hi,
I am trying to use do_dssp to generate a secondary structure map over time for
a 10-ns simulation. I have installed dssp_2.2.0 at the usual /usr/local/bin
I tried running it with the following command line
do_dssp -f md.xtc -s md.tpr -o ss.xpm -sc ss
Hi Michael,
After looking at the codes, it seems to me that the exchange scheme I
posted previously incurs violation of detailed balance, which seems to be a
bug. I'll really appreciate it if you can clarify this.
Let me re-state what I was trying to do. I have the following 7-component
restraint
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