On 14/05/2012 4:18 PM, Anirban wrote:
On Mon, May 14, 2012 at 11:35 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:
On 14/05/2012 3:52 PM, Anirban wrote:
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36
FF on GROAMCS4.5.5 on a parallel clust
On Mon, May 14, 2012 at 11:35 AM, Mark Abraham wrote:
> On 14/05/2012 3:52 PM, Anirban wrote:
>
> Hi ALL,
>
> I am trying to simulate a membrane protein system using CHARMM36 FF on
> GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
> arounf 1,17,000 atoms. The job runs f
On 14/05/2012 4:14 PM, bunty xy wrote:
Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
g
Hello friends,
I am facing problem in using DSSP.
I want the DSSP Plot.The lattest binary of DSSP does not generate DSSP
Plot ,It generate .dssp file,which have values .But i want the DSSP
PLot.Please tell me the installation procedure and download link to
get the dssp plot.
Thanks
bunty
--
gmx-
On 14/05/2012 3:52 PM, Anirban wrote:
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists
of arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120
cores) using mpirun and gives proper out
On 14/05/2012 2:24 PM, mohan maruthi sena wrote:
Hi all,
I want to define a potential form and give it as input for
which i have seen manual ,thought gromacs table option is fine, i have
an example of generating 9-6 potential form , My question is how to
generate table.xvg, what is
Hi ALL,
I am trying to simulate a membrane protein system using CHARMM36 FF on
GROAMCS4.5.5 on a parallel cluster running on MPI. The system consists of
arounf 1,17,000 atoms. The job runs fine on 5 nodes (5X12=120 cores) using
mpirun and gives proper output. But whenever I try to submit it on mor
Hi all,
I want to define a potential form and give it as input for which
i have seen manual ,thought gromacs table option is fine, i have an example
of generating 9-6 potential form , My question is how to generate
table.xvg, what is the command to generate table.xvg from code table.c.
>? > >>
>>? > >> [ angles ]
>>? > >> ; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
>>? > >> 2 1 3 1 123.4390 403.48 123.4390 403.48
>>? > >> 2 1 4 1 123.4390 403.48 123.4390 403.48
>>? > >>
>>? >
On 5/13/12 9:54 PM, Andrew DeYoung wrote:
Hi Justin,
Thanks so much! :-)
I checked, and I am using no constraints. However, what if I were? If I
did have constraints, then what would you recommend for the continuation
keyword?
Per the description in the manual, it should be set to "yes"
Hi Justin,
Thanks so much! :-)
I checked, and I am using no constraints. However, what if I were? If I
did have constraints, then what would you recommend for the continuation
keyword?
Thanks!
Andrew DeYoung
Carnegie Mellon University
---
If not using constraints, the continuation keyword
On 5/13/12 9:11 PM, Andrew DeYoung wrote:
Greetings,
I am running 5 ns of equilibration followed by 10 ns of production dynamics.
Equilibration and production dynamics differ only in the number of steps and
the frequency of saving the positions, velocities, forces, and energies. To
conserve d
Greetings,
I am running 5 ns of equilibration followed by 10 ns of production dynamics.
Equilibration and production dynamics differ only in the number of steps and
the frequency of saving the positions, velocities, forces, and energies. To
conserve disk space, I set nstxout = nstvout = nstfout =
On 5/13/12 2:17 PM, Shima Arasteh wrote:
But if the hydrogen has charge and its charge is not zero, then the total charge
of formyl wouldn't be zero! Make sense?
This is precisely why I've told you several times that you need to reconsider
how you've done your parameterization. If you run
But if the hydrogen has charge and its charge is not zero, then the total
charge of formyl wouldn't be zero! Make sense?
Sincerely,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sunday, May 13, 2012 9:44 PM
Subject: Re: [gmx-us
Thanks,
It was just a question and I prefer to use the CHARMM36.
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Sunday, May 13, 2012 9:44 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue
pairs
On 5/1
On 5/13/12 1:06 PM, Shima Arasteh wrote:
Even in gromos87, if I want to make a .rtp file for formyl, I need to put H atom
in it? I mean, defining all atoms of a residue is necessary? Aren't the hydrogen
atoms set by the gromacs package?
No. The presence of hydrogen atoms is set by the force
On 5/13/12 12:52 PM, Sangita Kachhap wrote:
Hello all
I am running GROMACS Tutorial: KALP15 in POPC
I have compeleted production run 1 ns now I want to extend it for next 1 ns.
For this I have used commond:
tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt
On 5/13/12 12:42 PM, Shima Arasteh wrote:
OK, so I entered the H atom corresponding to the structure and then changed the
file as below,
[ For ]
[ atoms ]
; name type charge charge group
C CTL1 0.5700 0
O O -0.5700 0
H HC 0.00 0
I find it highly unlikely that a zero charge should be assigne
Even in gromos87, if I want to make a .rtp file for formyl, I need to put H
atom in it? I mean, defining all atoms of a residue is necessary? Aren't the
hydrogen atoms set by the gromacs package?
Cheers,
Shima
From: Justin A. Lemkul
To: Discussion list for G
Hello all
I am running GROMACS Tutorial: KALP15 in POPC
I have compeleted production run 1 ns now I want to extend it for next 1 ns.
For this I have used commond:
tpbconv -s md_0_1.tpr -extend 1000 -o md_0_2.tpr
mdrun -s nmd_0_2.tpr -cpi md_0_1.cpt
I am getting files are:
ener.edr
md.log
state.c
OK, so I entered the H atom corresponding to the structure and then changed the
file as below,
[ For ]
[ atoms ]
; name type charge charge group
C CTL1 0.5700 0
O O -0.5700 0
H HC 0.00 0
[angles ]
ai
On 5/13/12 11:43 AM, Shima Arasteh wrote:
Again thanks for all your replies.
As I got through your advices, I found that the atoms contribute in making bonds
and angles in a residue , or make dihedrals in a residue ( or with atoms in next
ones) plus the charge of a the residue should be defined
Again thanks for all your replies.
As I got through your advices, I found that the atoms contribute in making
bonds and angles in a residue , or make dihedrals in a residue ( or with atoms
in next ones) plus the charge of a the residue should be defined properly in
.rtp files to define the new
Dear Justin,
Thank you very much from your response.
Best Regards
Dina
From: Justin A. Lemkul
To: dina dusti ; Discussion list for GROMACS users
Sent: Sunday, May 13, 2012 5:23 PM
Subject: Re: [gmx-users] dipole moment
On 5/13/12 8:41 AM, dina dusti wr
On 5/13/12 8:41 AM, dina dusti wrote:
Dear GROMACS Specialists,
I have one system consists of water and two other molecules. I work by MARTINI
CG force field. I want to calculate dipole moment of molecules in water.
May I ask you to help me, Please?
I doubt you can. Unless you are using ve
On 5/13/12 5:54 AM, Kowsar Bagherzadeh wrote:
Dear Users,
I am trying to generate an *.ITP file for a ligand I am studying using Prodrg
server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar
hydrogens) while the *.ITP file dispays 37 atoms and it does not display the
dou
Dear GROMACS Specialists,
I have one system consists of water and two other molecules. I work by MARTINI
CG force field. I want to calculate dipole moment of molecules in water.
May I ask you to help me, Please?
Best Regards
Dina
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.g
Dear Users,
I am trying to generate an *.ITP file for a ligand I am studying using Prodrg
server. but the DRGPOH.PDB it gives to me displays only 26 atoms ( with apolar
hydrogens) while the *.ITP file dispays 37 atoms and it does not display the
double bond in the structure, which results in a
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