Moeed wrote:
Dear Justin,
Thank you for your message. My objective is to calculate interaction
energies between polymer (polyethylene) and hydrocarbon solvent ( also
FE calculations). I am using rlist of 1.1 nm.
1- Do I need to increase rlist ( to 1.4 nm) to overcome the error message?
You need an rlist of sufficient size to provide a neighbor searching buffer.
This is described in the manual and has been discussed on this list within the
last few days.
2- As with the electrostatics treatment in my hydrocarbon system ( only
C and H) I was
unsure if I need to include electrostatics potentials (although there
exist partial charges).
I digged into the literature and found the following articles containing
nonpolar polymers
where vdw is the only nonbonded term in the FF. Thats why I switched
that term off. I appreciate your comments/idea on this.
You can't make ad hoc changes to force fields. I'd say that all you've done is
create an untested, arbitrarily modified version of OPLS. You should read the
primary literature for the force field (which hopefully you've already done),
and refer to charge assignment and the reasons for assigning partial charges to
hydrophobic groups. In real life, there are electrostatic terms as part of the
interactions between all atoms, including induced dipoles in hydrophobic groups.
Although we can't model these explicitly with non-polarizable force fields,
they still exist. Fixed-charge force fields attempt to replicate this real-life
behavior (with varied success).
http://pubs.acs.org/doi/abs/10.1021/ma9600419
This paper did not use OPLS, so its treatment of electrostatics is irrelevant.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TXW-40TY56F-16&_user=458507&_coverDate=11%2F30%2F2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1650178009&_rerunOrigin=google&_acct=C000022002&_version=1&_urlVersion=0&_userid=458507&md5=bf0b74cfc76e0dafbadf06396fb63745&searchtype=a
<http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TXW-40TY56F-16&_user=458507&_coverDate=11%2F30%2F2000&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1650178009&_rerunOrigin=google&_acct=C000022002&_version=1&_urlVersion=0&_userid=458507&md5=bf0b74cfc76e0dafbadf06396fb63745&searchtype=a>
This link did not work, so I cannot comment.
The point is that you should never make ad hoc changes to force fields. People
spend years (if not decades) creating and refining force field models that work,
and though you may find it convenient to ignore certain terms, you probably
shouldn't be. Any reviewer that critiques a paper that has such changes should
be very, very concerned about improper use of force fields.
-Justin
Thanks
Moeed
================================================
pbc = xyz
energygrps = PE HEX
; Run control
integrator = md
dt = 0.002
nsteps = 500000 ;5000
nstcomm = 100
; Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
; Neighbor searching
nstlist = 10
ns_type = grid
; Electrostatics/VdW
;;;;coulombtype = PME
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9 ;0
; Cut-offs
rlist = 1.1
rcoulomb = 1.1 ;1.0
rvdw = 1.0
; Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1 ;0.1
ref_t = 400 ;300
; Velocity generation
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = lincs
===================================================
On 28 February 2011 17:12, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Moeed wrote:
Dear experts,
Please kindly comment on this error. Thank you very much.
I am getting the known charge group radii error. (in 4.0.7
version with the same settings my simulations run with no error)
==========================
NOTE 1 [file md.mdp]:
The sum of the two largest charge group radii (0.205676) is
larger than
rlist (1.100000) - rvdw (1.000000)
There was 1 note
. . .
turning all bonds into constraints... turning all
bonds into constraints...
Largest charge group radii for Van der Waals: 0.103, 0.103 nm
This run will generate roughly 317 Mb of data
===================================
This error has been discussed several times on the archive after
release of 4.5.3. Please note that my charge groups are CH3 and
CH2 only! . To treat this error I dont know If I need to
increase rlist (as suggested in the first link below) or use
maxwarn -1 ( second link). How can I diagnose which one to choose?
http://lists.gromacs.org/pipermail/gmx-users/2011-January/057830.html
http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html
In the latter case, the problem was a result of groups being split
by PBC. This is not your problem. Be careful about taking posts
out of context.
It's usually better to increase rlist for proper energy
conservation. You haven't posted your .mdp file (which is usually
pretty important for understanding what's going on), but I'll assume
you're using some sort of switch or shift function for either van
der Waals or Coulombic interactions. In this case, the manual is
pretty clear about proper use, although you appear to not be using
any charges at all. How does that make sense? What is your
objective? Even OPLS hydrophobic moieties should have small partial
charges across C-H bonds.
-Justin
==================================================
charge groups of solute:
1 opls_135 1 EthB C1 1 0
12.011 ; qtot 0
2 opls_140 1 EthB H11 1 0
1.008 ; qtot 0
3 opls_140 1 EthB H12 1 0
1.008 ; qtot 0
4 opls_140 1 EthB H13 1 0
1.008 ; qtot 0
5 opls_136 1 EthB C2 2 0
12.011 ; qtot 0
6 opls_140 1 EthB H21 2 0
1.008 ; qtot 0
7 opls_140 1 EthB H22 2 0
1.008 ; qtot 0
8 opls_136 1 EthB C3 3 0
12.011 ; qtot 0
9 opls_140 1 EthB H31 3 0
1.008 ; qtot 0
10 opls_140 1 EthB H32 3 0
1.008 ; qtot 0
11 opls_136 1 EthB C4 4 0
12.011 ; qtot 0
12 opls_140 1 EthB H41 4 0
1.008 ; qtot 0
13 opls_140 1 EthB H42 4 0
1.008 ; qtot 0
==================================
Thanks
moeed
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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--
Moeed Shahamat
Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php
Web:http://mmrg.chemeng.mcgill.ca/
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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