[gmx-users] I have questions for tabulated bonded potentials
Chang Woon Jang
changwoonjang at gmail.com
Wed Aug 31 02:40:11 CEST 2016
Do you mean "Order of parameters"? If I would like to specify for
table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for
table_b2.xvg, I need to set 2 after 8.
Am I right?
On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang <changwoonjang at gmail.com>
> Dear Justin Lemkul,
> I have seen the 4.2.12 and Table 5.5. However, it does not show the
> specific example for several tabulated potentials in topol.top file. I
> created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
> table_a2.xvg ... table_a6.xvg, table_d1.xvg .... table_d4.xvg. Those are
> different n values for each interactions.
> However, 4.2.12 just says that "Multiple tables can be supplied simply by
> using different values of n, and are applied to the appropriate bonds, as
> specified in the topology (Table 5.5)".
> In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
> no explanation for distingushing several tables to specify different bonded
> Thank you.
> Best regards,
> Changwoon Jang
> On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>>> Dear Gromacs Users,
>>> From the above question, I think that I need to specify the each
>>> bonded interaction in topol.top file. Am I right?
>>> For example,
>>> [ bond ]
>>> 1 1 2 table_b1.xvg
>>> 2 2 3 table_b2.xvg
>>> 3 3 4 table_b3.xvg
>>> Is this right format if I have several tabulated potential files in
>> No. Consult Table 5.5 - the function type is 8 (or 9, depending on
>> whether you need to generate exclusions) and the table number is supplied
>> as one of the parameters. See also section 4.2.14.
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
> Best regards,
> Changwoon Jang,
> Postdoctoral Research Fellow
> Department of Chemical & Biological Engineering, Drexel University
> 3141 Chestnut Street, Philadelphia, PA 19104
> Voice: (662) 617-2267
> E-mail: cj395 at drexel.edu
Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104
Voice: (662) 617-2267
E-mail: cj395 at drexel.edu
More information about the gromacs.org_gmx-users