[gmx-users] how to simulate a line charge
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 14 23:07:19 CEST 2011
Amit Choubey wrote:
> sorry i did not mention it but the E field contribution should be zero,
> i am sure about it. Also when i make all the cutoff = 0 the energy terms are
> 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 1.03128e+06 1.03128e+06
> Pressure (bar)
> 0.00000e+00
>
> Step Time Lambda
> 1 1.00000 0.00000
>
> Energies (kJ/mol)
> Bond Angle LJ (SR) Coulomb (SR) Potential
> 7.49142e-02 0.00000e+00 0.00000e+00 1.03104e+06 1.03104e+06
> Pressure (bar)
> 0.00000e+00
>
> Coulomb (SR) is quite close but not exactly equal to previous case when
> cutoff is 60 nm.
>
Then I guess in this case you're getting intra-charge group short-range
interactions, which I hadn't considered before. In the case of a ridiculously
large charge group, atoms may be in the same group but outside the cutoff, in
which case they would contribute to Coulomb (SR). Not a typical case.
-Justin
> On Sun, Aug 14, 2011 at 1:57 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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>
> <mailto: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>>
> <mailto: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>>
> <mailto: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>
> <http://vt.edu> |
>
> (540) 231-9080 <tel:%28540%29%20231-9080>
> <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>
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> <http://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> <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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