Re: [gmx-users] Cutoff Parameters

[Justin A. Lemkul]

There are lots of discussions on this topic in the list archive.  See, for 
example:

http://www.gromacs.org/pipermail/gmx-users/2002-August/002320.html

-Justin

Soumik Banerjee wrote:

Hi,

I am sorry that I am repeating an earlier email that I sent out to the 
list. I did not receive a reply. It would indeed be very useful for me 
to have some input on this.


I am new to gromacs and have a pretty basic question. I am using 
gromacs-3.3.3 to simulate glycine crystal growth. My system consists of 
glycine crystal surrounded by a solution of glycine in water (system 
size: 4.28 by 5.76 by 3.27 nm^3). I have been trying to find appropriate 
values for the cutoff distances (rvdw, rcoulomb) and corresponding 
rlist. I use GROMOS96 43a1 force field with PME (pme_order = 4, rtol = 
1e-5).


The examples given in the gromacs tutorial use rvdw = rlist = rcoulomb = 
0.9 (with coulombtype = cutoff). I also found a couple of relevant 
journal articles that used these parameters. A relevant message on the 
archive 
(http://osdir.com/ml/science.biology.gromacs.user/2006-06/msg00389.html) 
suggests the use of these parameters. Also, "Using PME" on page 78 of 
the manual 3.3 suggests rvdw = rlist = rcoulomb = 0.9


However, the manual suggests rvdw = 1.4 for grmos96 force field. When I 
did a gmx-users list search, I found some mdp files from various users 
that use vdw = rlist = rcoulomb = 0.9/1.0.


Based on sections 7.3.9 and 7.3.10, I think rlist = rcoulomb = 0.9, and 
rvdw = 1.4 would be appropriate. However, I am not completely sure and 
it would be great if someone can please recommend a set of values for 
these parameters (rlist, rvdw, rcoulomb) for coulombtype = PME.


Best,
Soumik

*Soumik Banerjee
*
Max-Planck-Institute
for Dynamics of Complex Technical Systems
Sandtorstraße 1
39106 Magdeburg
Germany
Email: [EMAIL PROTECTED]
Phone: +49 391 6110 163







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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Cutoff Parameters

[Soumik Banerjee]

Hi,

I am sorry that I am repeating an earlier email that I sent out to the list. I 
did not receive a reply. It would indeed be very useful for me to have some 
input on this.

I am new to gromacs and have a pretty basic question. I am
using gromacs-3.3.3 to simulate glycine crystal growth. My system
consists of glycine crystal surrounded by a solution of glycine in
water (system size: 4.28 by 5.76 by 3.27 nm^3). I have been trying to
find appropriate values for the cutoff distances (rvdw, rcoulomb) and
corresponding rlist. I use GROMOS96 43a1 force field with PME
(pme_order = 4, rtol = 1e-5). 

The examples given in the
gromacs tutorial use rvdw = rlist = rcoulomb = 0.9 (with coulombtype =
cutoff). I also found a couple of relevant journal articles that used
these parameters. A relevant message on the archive 
(http://osdir.com/ml/science.biology.gromacs.user/2006-06/msg00389.html) 
suggests the use of these parameters. Also,
"Using PME" on page 78 of the manual 3.3 suggests rvdw = rlist =
rcoulomb = 0.9

However, the manual suggests rvdw = 1.4 for grmos96
force field. When I did a gmx-users list search, I found some mdp files
from various users that use vdw = rlist = rcoulomb = 0.9/1.0. 

Based on
sections 7.3.9 and 7.3.10, I think rlist = rcoulomb = 0.9, and rvdw =
1.4 would be appropriate. However, I am not completely sure and it
would be great if someone can please recommend a set of values for
these parameters (rlist, rvdw, rcoulomb) for coulombtype = PME. 

Best,
Soumik

Soumik Banerjee
Max-Planck-Institute
for Dynamics of Complex Technical Systems
Sandtorstraße 1
39106 Magdeburg
Germany
Email: [EMAIL PROTECTED]
Phone: +49 391 6110 163 




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[gmx-users] Cutoff Parameters

[Soumik Banerjee]

Hi,

I am new to gromacs and have a pretty basic question. I am using gromacs-3.3.3 
to simulate glycine crystal growth. My system consists of glycine crystal 
surrounded by a solution of glycine in water (system size: 4.28 by 5.76 by 3.27 
nm^3). I have been trying to find appropriate values for the cutoff distances 
(rvdw, rcoulomb) and corresponding rlist. I use GROMOS96 43a1 force field with 
PME  (pme_order = 4, rtol = 1e-5). 

The examples given in the gromacs tutorial use rvdw = rlist = rcoulomb = 0.9 
(with coulombtype = cutoff). I also found a couple of relevant journal articles 
that used these parameters. However, the manual suggests rvdw = 1.4 for grmos96 
force field. When I did a gmx-users list search, I found some mdp files from 
various users that use vdw = rlist = rcoulomb = 0.9/1.0. Also, "Using PME" on 
page 78 of the manual 3.3 suggests rvdw = rlist = rcoulomb = 0.9

Based on sections 7.3.9 and 7.3.10, I think rlist = rcoulomb = 0.9, and rvdw = 
1.4 would be appropriate. However, I am not completely sure and it would be 
great if someone can please recommend a set of values for these parameters 
(rlist, rvdw, rcoulomb) for coulombtype = PME. 

Best,
Soumik

Soumik BanerjeeMax-Planck-Institute
for Dynamics of Complex Technical Systems
Sandtorstraße 1
39106 Magdeburg
Germany
Email: [EMAIL PROTECTED]
Phone: +49 391 6110 163 




  ___
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
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