[gmx-users] charge group radii- use maxwarn or increase rlist?
Moeed
lecielll at googlemail.com
Tue Mar 1 00:22:11 CET 2011
Thank you for your helpful comments. I am totally convinced that I was not
using proper force field.
Best,
moeed
On 28 February 2011 18:12, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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 <jalemkul at vt.edu <mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>.
>>
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
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/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110228/c328f464/attachment.html>
More information about the gromacs.org_gmx-users
mailing list