Thank you for your helpful comments. I am totally convinced that I was not using proper force field. <br><br>Best,<br>moeed<br><br><br><br><div class="gmail_quote">On 28 February 2011 18:12, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Moeed wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Justin,<br>
<br>
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.<br>
<br>
1- Do I need to increase rlist ( to 1.4 nm) to overcome the error message?<br>
<br>
</blockquote>
<br></div>
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.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2- As with the electrostatics treatment in my hydrocarbon system ( only C and H) I was<br>
unsure if I need to include electrostatics potentials (although there exist partial charges).<br>
I digged into the literature and found the following articles containing nonpolar polymers<br>
where vdw is the only nonbonded term in the FF. Thats why I switched that term off. I appreciate your comments/idea on this.<br>
<br>
<br>
</blockquote>
<br></div>
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).<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<a href="http://pubs.acs.org/doi/abs/10.1021/ma9600419" target="_blank">http://pubs.acs.org/doi/abs/10.1021/ma9600419</a><br>
<br>
</blockquote>
<br></div>
This paper did not use OPLS, so its treatment of electrostatics is irrelevant.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<a href="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" target="_blank">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</a> <<a href="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" target="_blank">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</a>><br>
<br>
</blockquote>
<br>
This link did not work, so I cannot comment.<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><div></div><div class="h5">
<br>
Thanks<br>
Moeed<br>
<br>
<br>
================================================<br>
<br>
pbc = xyz<br>
energygrps = PE HEX<br>
<br>
; Run control<br>
integrator = md<br>
dt = 0.002<br>
nsteps = 500000 ;5000<br>
nstcomm = 100<br>
<br>
; Output control<br>
nstenergy = 100<br>
nstxout = 100<br>
nstvout = 0<br>
nstfout = 0<br>
nstlog = 1000<br>
nstxtcout = 1000<br>
<br>
; Neighbor searching<br>
nstlist = 10<br>
ns_type = grid<br>
<br>
; Electrostatics/VdW<br>
;;;;coulombtype = PME<br>
vdw-type = Shift<br>
rcoulomb-switch = 0<br>
rvdw-switch = 0.9 ;0<br>
<br>
; Cut-offs<br>
rlist = 1.1<br>
rcoulomb = 1.1 ;1.0<br>
rvdw = 1.0<br>
<br>
; Temperature coupling<br>
Tcoupl = v-rescale<br>
tc-grps = System<br>
tau_t = 0.1 ;0.1<br>
ref_t = 400 ;300<br>
<br>
<br>
; Velocity generation<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
; Bonds<br>
constraints = all-bonds<br>
constraint-algorithm = lincs<br>
<br>
===================================================<br>
<br>
<br>
<br>
<br></div></div><div><div></div><div class="h5">
On 28 February 2011 17:12, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Moeed wrote:<br>
<br>
Dear experts,<br>
<br>
Please kindly comment on this error. Thank you very much.<br>
<br>
I am getting the known charge group radii error. (in 4.0.7<br>
version with the same settings my simulations run with no error)<br>
<br>
==========================<br>
NOTE 1 [file md.mdp]:<br>
The sum of the two largest charge group radii (0.205676) is<br>
larger than<br>
rlist (1.100000) - rvdw (1.000000)<br>
<br>
There was 1 note<br>
. . .<br>
<br>
turning all bonds into constraints... turning all<br>
bonds into constraints...<br>
Largest charge group radii for Van der Waals: 0.103, 0.103 nm This run will generate roughly 317 Mb of data<br>
<br>
===================================<br>
<br>
This error has been discussed several times on the archive after<br>
release of 4.5.3. Please note that my charge groups are CH3 and<br>
CH2 only! . To treat this error I dont know If I need to<br>
increase rlist (as suggested in the first link below) or use<br>
maxwarn -1 ( second link). How can I diagnose which one to choose?<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-January/057830.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-January/057830.html</a><br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html</a><br>
<br>
<br>
In the latter case, the problem was a result of groups being split<br>
by PBC. This is not your problem. Be careful about taking posts<br>
out of context.<br>
<br>
It's usually better to increase rlist for proper energy<br>
conservation. You haven't posted your .mdp file (which is usually<br>
pretty important for understanding what's going on), but I'll assume<br>
you're using some sort of switch or shift function for either van<br>
der Waals or Coulombic interactions. In this case, the manual is<br>
pretty clear about proper use, although you appear to not be using<br>
any charges at all. How does that make sense? What is your<br>
objective? Even OPLS hydrophobic moieties should have small partial<br>
charges across C-H bonds.<br>
<br>
-Justin<br>
<br>
<br>
==================================================<br>
charge groups of solute:<br>
<br>
1 opls_135 1 EthB C1 1 0 12.011 ; qtot 0<br>
2 opls_140 1 EthB H11 1 0 1.008 ; qtot 0<br>
3 opls_140 1 EthB H12 1 0 1.008 ; qtot 0<br>
4 opls_140 1 EthB H13 1 0 1.008 ; qtot 0<br>
5 opls_136 1 EthB C2 2 0 12.011 ; qtot 0<br>
6 opls_140 1 EthB H21 2 0 1.008 ; qtot 0<br>
7 opls_140 1 EthB H22 2 0 1.008 ; qtot 0<br>
8 opls_136 1 EthB C3 3 0 12.011 ; qtot 0<br>
9 opls_140 1 EthB H31 3 0 1.008 ; qtot 0<br>
10 opls_140 1 EthB H32 3 0 1.008 ; qtot 0<br>
11 opls_136 1 EthB C4 4 0 12.011 ; qtot 0<br>
12 opls_140 1 EthB H41 4 0 1.008 ; qtot 0<br>
13 opls_140 1 EthB H42 4 0 1.008 ; qtot 0<br>
<br>
==================================<br>
<br>
Thanks<br>
moeed<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
<br>
<br>
-- <br>
Moeed Shahamat<br>
Graduate Student (Materials Modeling Research Group)<br>
McGill University- Department of Chemical Engineering<br>
Montreal, Quebec H3A 2B2, Canada<br>
Web:<a href="http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php" target="_blank">http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php</a><br>
Web:<a href="http://mmrg.chemeng.mcgill.ca/" target="_blank">http://mmrg.chemeng.mcgill.ca/</a><br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Moeed Shahamat<br>Graduate Student (Materials Modeling Research Group)<br>McGill University- Department of Chemical Engineering<br>Montreal, Quebec H3A 2B2, Canada<br>
Web:<a href="http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php">http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php</a><br>Web:<a href="http://mmrg.chemeng.mcgill.ca/">http://mmrg.chemeng.mcgill.ca/</a><br>