[gmx-users] charge group radii- use maxwarn or increase rlist?
Moeed
lecielll at googlemail.com
Mon Feb 28 23:48:53 CET 2011
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?
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.
http://pubs.acs.org/doi/abs/10.1021/ma9600419
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
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 <jalemkul at vt.edu> 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 | (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/
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