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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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.a...@gmail.com <mailto:kgp.a...@gmail.com>
<mailto:kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>>
<mailto:kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>
<mailto:kgp.a...@gmail.com <mailto:kgp.a...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
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Department of Biochemistry
Virginia Tech
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