[gmx-users] how to simulate a line charge
Amit Choubey
kgp.amit at gmail.com
Sun Aug 14 22:51:49 CEST 2011
Following is the mdp file
cpp = /usr/bin/cpp
;define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 10000
;
; Energy minimizing stuff
;
emtol = 200
emstep = 0.01
pbc = no
nstcomm = 0
ns_type = grid
coulombtype = Cut-off
rlist = 60
rcoulomb = 60
rvdw = 60
Tcoupl = no
Pcoupl = no
gen_vel = no
E_x = 1 0 0
E_y = 1 0 0
E_z = 1 0 0
Following is the energy term
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Angle LJ (SR) Coulomb (SR) Potential
1.11496e-07 0.00000e+00 0.00000e+00 9.90561e+05 9.90561e+05
Pressure (bar)
0.00000e+00
Step Time Lambda
1 1.00000 0.00000
Energies (kJ/mol)
Bond Angle LJ (SR) Coulomb (SR) Potential
7.55922e-02 0.00000e+00 0.00000e+00 9.90324e+05 9.90324e+05
Pressure (bar)
0.00000e+00
Amit
On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Amit Choubey wrote:
>
>> Justin, when i define the whole line charge as a charge group i do get a
>> coulomb energy contribution. I thought there would be no non-bonded
>> contribution. I use a very high cut-off (longer than chain length) and no
>> pbc. Am i missing something ?
>>
>>
> Without seeing your .mdp file and the actual energy terms you're observing,
> I can only guess. One would think that if it is the only molecule in the
> system, there should be no intermolecular Coulombic terms (unless maybe some
> arise due to periodicity, but in that case you do not have an infinite
> system and then they are artifacts). There may be intramolecular terms
> (like 1-4) or PME-related terms.
>
> -Justin
>
> On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey <kgp.amit at gmail.com<mailto:
>> kgp.amit at gmail.com>> wrote:
>>
>> I was not sure if changing the size of maxcg would not negatively
>> influence anything else. I will give it a try. Thanks Justin
>>
>>
>> On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Amit Choubey wrote:
>>
>> I change the maximum charge group size defined in the
>> include/types/nblist.h header from 32 to 267. Then grompp
>> worked fine but the mdrun did not start. The following error
>> came out
>>
>> Program mdrun_jptlc, VERSION 4.5.3
>> Source code file: ns.c, line: 2417
>>
>> Fatal error:
>> Max #atoms in a charge group: 267 > 64
>>
>>
>> /* Verify whether largest charge group is <= max cg.*
>> * This is determined by the type of the local exclusion
>> type *
>> * Exclusions are stored in bits. (If the type is not
>> large*
>> * enough, enlarge it, unsigned char -> unsigned short
>> -> unsigned long)*
>> */
>>
>>
>> The solution is described in the comment above.
>>
>>
>> maxcg = sizeof(t_excl)*8;
>>
>>
>> Increase the size here.
>>
>> -Justin
>>
>>
>> if (nr_in_cg > maxcg)
>> {
>> gmx_fatal(FARGS,"Max #atoms in a charge group: %d >
>> %d\n",
>> nr_in_cg,maxcg);
>> }
>>
>>
>> -- ==============================**__==========
>>
>> 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
>> <tel:%28540%29%20231-9080>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/__mailman/listinfo/gmx-users>
>> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >
>> Please search the archive at
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search>
>> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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@**gromacs.org<gmx-users-request at gromacs.org>
>> >.
>>
>> Can't post? Read http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists>
>> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>> >
>>
>>
>>
>>
> --
> ==============================**==========
>
> 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110814/67f1a462/attachment.html>
More information about the gromacs.org_gmx-users
mailing list