[gmx-users] how to simulate a line charge
Amit Choubey
kgp.amit at gmail.com
Sun Aug 14 23:04:25 CEST 2011
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.
On Sun, Aug 14, 2011 at 1:57 PM, Justin A. Lemkul <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>> 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://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>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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