[gmx-users] how to simulate a line charge
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 14 22:57:37 CEST 2011
Amit Choubey wrote:
> 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
>
>
I suspect that energy terms comes from the use of an electric field, which you
had not mentioned before.
-Justin
> Amit
>
> On Sun, Aug 14, 2011 at 1:23 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>
> <mailto: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> <http://vt.edu> |
> (540) 231-9080 <tel:%28540%29%20231-9080>
> <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>>
>
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> --
> ==============================__==========
>
> 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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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--
========================================
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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