Hello all
I have to create an octane box for studying effect of solvent hydrophobicity
on enzyme activation.
Anyone using octane parameterized file in amber?
Please suggest me how to parameterize it or is there any tutorial for it.
As i am a beginner, so plz explain in steps.
Thanks a lot.
Yuvraj
On Mon, Dec 6, 2010 at 6:05 PM, gmx-users-requ...@gromacs.org wrote:
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Today's Topics:
1. Re: Constraining two virtual sites (Mark Abraham)
2. Re: Help - LINCS WARNING: bonds that rotated more than30
degrees (Justin A. Lemkul)
3. RE: Constraining two virtual sites (Berk Hess)
-- Forwarded message --
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Mon, 06 Dec 2010 22:31:55 +1100
Subject: Re: [gmx-users] Constraining two virtual sites
On 6/12/2010 9:43 PM, Sebastian Fritsch wrote:
Hi everybody,
I have some trouble setting up topology for my, I admit, quite unusual
system. I need to constrain the center of masses of two groups of atoms to a
fixed 'bond' length. Since I have to do this for every molecule I cannot use
the 'pull constraint' of the free energy code.
Thus in my topology I defined a com vsite for each group and tried to
apply a constraint between them. The atoms within each group are connected
by harmonic springs forming a ring polymer (for those of you who know it:
this is supposed to become the path integral representation in the end...)
The topol.top for a single molecule test system looks like this:
[ defaults ]
; nbfunc comb-rulegen-pairsfudgeLJfudgeQQ
1 1no1.01.0
[ atomtypes ]
;name masschargeptype C6 C12 ; sigma
epsilon
A 1.00800 0 A 0 0
B 1.00800 0 A 0 0
C 1.00800 0 A 0 0
VS 0.000 0 V 0 0
[ moleculetype ]
; molname nrexcl
SOL0
[ atoms ]
; id at resnr resnm atnm cgnr charge
1 VS1 A V11 0
2 VS1 B V22 0
3 A 1 A A 3 0 4 B 1 A B
4 0 5 C 1 A C 5 0 6 A 1 B
A 6 0 7 B 1 B B 7 0 8
C 1 B C 8 0 [ virtual_sitesN ]
;
1 2 3 4 5
2 2 6 7 8
[ bonds ]
; ai aj
3 4 1 0 1687
4 5 1 0 1687
5 3 1 0 1687
6 7 1 0 1687
7 8 1 0 1687
8 6 1 0 1687
[ constraints ]
; ai aj funct length_A
1 2 1 0.1633
[ system ]
TEST
[ molecules ]
SOL 1
The conf.gro is setup such that the constraint is satisfied initially.
When I run the simulation with LINCS the constraint seem to be not applied
at all, the distance beetween the two vsites increases just as in free
diffusion. With SHAKE the system explodes immediately (without error
message, but every value is inf or nan).
I am running the system with the sd integrator in (vers. 4.5.3) but also
tried md and no thermostat, with no change in results.
I appreciate any advice on this!
Thanks,
Sebastian
I can't see anything that looks wrong. Make sure you inspect the output of
grompp thoroughly for clues about how it's interpreting the .top file. You
may like to use gmxcheck to compare the .tpr files produced under various
permutations to see that things look like they're working correctly
(remember atom numbers will start from zero in the output). Try putting the
virtual site atoms after the real atoms in the ordering.
Mark
-- Forwarded message --
From: Justin A. Lemkul jalem...@vt.edu
To: YUVRAJ UBOVEJA yuvraj.ubov...@students.iiit.ac.in, Gromacs Users'
List gmx-users@gromacs.org
Date: Mon, 06 Dec 2010 07:31:08 -0500
Subject: [gmx-users] Re: Help - LINCS WARNING: bonds that rotated more than
30 degrees
Please keep all Gromacs-related correspondence on the gmx-users list. I am
not a private help service. I am CC'ing the list and would ask that
anything further be posted there.
Before posting anything to the list, check the list archive. Your problem
has been posted and answered literally thousands of times. Even better, the
Gromacs site is full of helpful information, like the following:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
YUVRAJ UBOVEJA
