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>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>
<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>
<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><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 class="gmail_quote">On 28 February 2011 17:12, 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 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 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 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 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 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?<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>
</blockquote>
<br></div>
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.<br>
<br>
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.<br>
<br>
-Justin<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;">
==================================================<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>
</blockquote>
<br></div>
-- <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>
========================================<br><font color="#888888">
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</font></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>