Thank you
Rituraj
On Wed, Jun 3, 2009 at 9:05 PM, <[email protected]
<mailto:[email protected]>> wrote:
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Today's Topics:
1. protein running out of box (sheerychen)
2. Re: protein running out of box (Justin A. Lemkul)
3. Re: protein running out of box (ravi sharma)
4. spc.itp for the amber force field (Rebeca Garc?a Fandi?o)
5. Some questions regarding generating topologies (Manik Mayur)
6. Re: Some questions regarding generating topologies
(Justin A. Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Wed, 3 Jun 2009 15:37:57 +0200
From: sheerychen <[email protected] <mailto:[email protected]>>
Subject: [gmx-users] protein running out of box
To: [email protected] <mailto:[email protected]>
Message-ID:
<[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset="iso-8859-1"
Hello, every body. I have running a MD for 10ns. However, after 5ns
part of
protein will running out of the box and be located at other part of the
water box. And the whole structure seems ver strange. It seems that
it was
caused by the mass translation but I have used the
comm_mode=Linear. Any
suggestions?
--
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071,
Hamburg,Germany
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: [email protected]
<mailto:[email protected]>
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Message: 2
Date: Wed, 03 Jun 2009 09:46:08 -0400
From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] protein running out of box
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected] <mailto:[email protected]>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
sheerychen wrote:
> Hello, every body. I have running a MD for 10ns. However, after
5ns part
> of protein will running out of the box and be located at other
part of
> the water box. And the whole structure seems ver strange. It
seems that
> it was caused by the mass translation but I have used the
> comm_mode=Linear. Any suggestions?
>
What you are seeing is a normal consequence of periodicity. There
is no "side"
in an infinite system:
http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions
-Justin
> --
> Zhen Chen,
> Department of Bioprocess and Biosystem Engineering,
> Hamburg University of Technology, Denickestr. 15, D-21071,
Hamburg,Germany
> Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail:
[email protected] <mailto:[email protected]>
> <mailto:[email protected] <mailto:[email protected]>>
>
>
>
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>
> _______________________________________________
> gmx-users mailing list [email protected]
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> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Wed, 3 Jun 2009 07:07:57 -0700 (PDT)
From: ravi sharma <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] protein running out of box
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset="iso-8859-1"
Dear Zhen Chen
Protein is located stranger(sometime at the one side of the
protein,in other frame other side). Its not a problem. Your
simulation is fine. it is due to you had given PBC. thats why. You
can reset your trejectory using trjconv.
regards
Ravi Datta Sharma Lecturer, Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
--- On Wed, 3/6/09, sheerychen <[email protected]
<mailto:[email protected]>> wrote:
From: sheerychen <[email protected] <mailto:[email protected]>>
Subject: [gmx-users] protein running out of box
To: [email protected] <mailto:[email protected]>
Date: Wednesday, 3 June, 2009, 7:07 PM
Hello, every body. I have running a MD for 10ns. However, after 5ns
part of protein will running out of the box and be located at other
part of the water box. And the whole structure seems ver strange. It
seems that it was caused by the mass translation but I have used
the comm_mode=Linear. Any suggestions?
--
Zhen Chen,
Department of Bioprocess and Biosystem Engineering,
Hamburg University of Technology, Denickestr. 15, D-21071,
Hamburg,Germany
Tel.: ++49 (0) 40 42878-3172, Fax: -3172, e-mail: [email protected]
<mailto:[email protected]>
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Message: 4
Date: Wed, 3 Jun 2009 14:43:09 +0000
From: Rebeca Garc?a Fandi?o <[email protected]
<mailto:[email protected]>>
Subject: [gmx-users] spc.itp for the amber force field
To: <[email protected] <mailto:[email protected]>>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I am trying to simulate a system using the parameters for ions
developed by Joung et al. and implemented in Amber (frcmod.ionsjc_spce).
I have the topology and the crd file. Now, I want to obtain the
topology for Gromacs using amb2gmx.pl, so I must change the default
parameters (for tip3p) included in amb2gmx.pl.
I have seen that in the .tar file ffamber_v4.0 there is no a
corresponding itp file for spc model of water in amber, so what
parameters should I include for the section of bondtypes,
angletypes, atoms, bonds, angles, settles,...? Those corresponding
to the SCP in Gromacs directly?
Thank you very much for your help.
Best wishes,
Rebeca Garcia
Academic Visitor
Oxford University
_________________________________________________________________
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Message: 5
Date: Wed, 3 Jun 2009 20:57:57 +0530
From: Manik Mayur <[email protected] <mailto:[email protected]>>
Subject: [gmx-users] Some questions regarding generating topologies
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID:
<[email protected]
<mailto:[email protected]>>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
Even though after going through the manual, I still have some basic
confusions regarding generating topologies.
1) I have generated an itp file after adding some Cl- ions using
genion. It
goes like this:
[ moleculetype ]
; Name nrexcl
Cl_ion 0
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 CL- 1 Cl- Cl 1 -1 35.453
; qtot
-1
2 CL- 2 Cl- Cl 2 -1 35.453
; qtot
-2
3 CL- 3 Cl- Cl 3 -1 35.453
; qtot
-3
........
........
To allow nb interactions between all the atoms in the molecule
Cl_ion, is
setting nrexcl = 0 okay?
2) In spce.itp provided with GROMACS,
[ moleculetype ]
; molname nrexcl
SOL 2
while in the manual, on pg. 100 (Chapter-5 Topologies)
[ moleculetype ]
; molname nrexcl
SOL 1
why is the inconsistency?
3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is
recommended).
Since SPC/E is one of the most used model, should I consider using OPLS
rather than GROMOS96, otherwise how significant will be the errors?
4) I am using GROMOS96 43a1, so am I allowed to change combination
rule to
'2' ( '1' is the default). How significantly will it affect the
simulations?
Any relevant idea/suggestion/reference is appreciated.
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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------------------------------
Message: 6
Date: Wed, 03 Jun 2009 11:34:34 -0400
From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] Some questions regarding generating
topologies
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected] <mailto:[email protected]>>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Manik Mayur wrote:
> Hi,
>
> Even though after going through the manual, I still have some basic
> confusions regarding generating topologies.
>
> 1) I have generated an itp file after adding some Cl- ions using
genion.
> It goes like this:
>
This is unnecessary. Just #include "ions.itp" and the parameters
for Cl- for
whatever force field you're using are included.
> [ moleculetype ]
> ; Name nrexcl
> Cl_ion 0
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 CL- 1 Cl- Cl 1 -1
35.453 ;
> qtot -1
> 2 CL- 2 Cl- Cl 2 -1
35.453 ;
> qtot -2
> 3 CL- 3 Cl- Cl 3 -1
35.453 ;
> qtot -3
> ........
> ........
>
> To allow nb interactions between all the atoms in the molecule
Cl_ion,
> is setting nrexcl = 0 okay?
>
> 2) In spce.itp provided with GROMACS,
>
> [ moleculetype ]
> ; molname nrexcl
> SOL 2
>
> while in the manual, on pg. 100 (Chapter-5 Topologies)
> [ moleculetype ]
> ; molname nrexcl
> SOL 1
>
> why is the inconsistency?
>
Probably just a typo.
> 3) I am using SPC/E water model with GROMOS96 43a1 ff, (SPC is
> recommended). Since SPC/E is one of the most used model, should I
> consider using OPLS rather than GROMOS96, otherwise how
significant will
> be the errors?
>
An excellent comparison of different force fields and different
water models can
be found in:
Hess and van der Vegt (2006) J. Phys. Chem. B 110: 17616-17626.
> 4) I am using GROMOS96 43a1, so am I allowed to change
combination rule
> to '2' ( '1' is the default). How significantly will it affect the
> simulations?
>
I would say it invalidates everything. The defaults for combination
rules,
bonded parameters, etc. are as much a part of each force field as
the atom types
and charges.
-Justin
> Any relevant idea/suggestion/reference is appreciated.
>
> Thanks,
>
> Manik Mayur
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
> INDIA
>
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list [email protected]
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> Please search the archive at http://www.gromacs.org/search before
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> www interface or send it to [email protected]
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
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