On 7/31/18 2:05 PM, RAHUL SURESH wrote:
Hi Dr. Mark
The itp file is as follows.
[ moleculetype ]
; Name nrexcl
FLU1 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_786 1 FLU1 F 0 0
18.99840
2 opls_786 1 FLU1 F 0 0
18.99840
[ bonds ]
; ai aj funct
1 2 1 ; F F
What parameters have you assigned for this bond?
[ pairs ]
; ai aj funct
1 2
Why are you assigning a pair interaction? These are for 1-4
interactions. If you're adding a pair, you're going to get a huge LJ
repulsion between your atoms that overwhelms the bonded potential, which
may be the cause of your problem.
-Justin
[ angles ]
; ai aj ak funct
[ dihedrals ]
; ai aj ak al funct
The atom type is chosen based on the sigma and epsilon values from the
paper attached to previous mail. [ pre-existing atom type ]
The atom didnt move much further but on equilibration the atoms are totally
dispersed.
On Tue, Jul 31, 2018 at 10:58 PM, Mark Abraham <[email protected]>
wrote:
Hi,
We can't tell without seeing your molecule type for F2. Presumably there is
no bond or the bond is too weak. How far do they move apart?
Mark
On Tue, Jul 31, 2018, 14:49 RAHUL SURESH <[email protected]> wrote:
Hi.
I obtained the LJ parameters from the paper *10.1007/s10765-009-0624-0. [
OPLS_786 ]*
Add the bond length and harmonic constraints from in ffbonded.itp
The charge is changed to 0 in the itp file and added to .top file.
Minimizations are executed without any error. But on examining the gro
file
from minimization, the fluorine molecules are broken into atoms. [ ie
they
atoms move away ]
Why is this happening?
On Mon, Jul 30, 2018 at 6:17 PM, Justin Lemkul <[email protected]> wrote:
On 7/30/18 5:54 AM, RAHUL SURESH wrote:
Hello users.
I overcame the warning errors. The naming is correct now. I tried to
update
the parameters for ffbonded.itp but how will I find the Kb value for
F-F ?
Vibrational frequency analysis.
Be careful generating the topology in the manner you have; the F
parameters come from trifluoroethanol, so the LJ parameters may not be
what
you want. And the charge of both F atoms in F2 should be set to zero
(note
that TopolGen is a dumb script that just looks for similarity; the
resulting topologies often require lots of changes).
-Justin
On Sat, 28 Jul 2018 at 6:52 PM, RAHUL SURESH <[email protected]>
wrote:
Hi all
I am performing a simulation between a protein and Fluorine
molecule. I
have optimized the F2 structure using Gaussian and inserted into the
box
using gmx insert-molecules command after adding solvent [gmx
solvate].
The
topology for fluorine molecule is generated by topolgen.
*[ moleculetype ]; Name nrexclFLU1 3[ atoms
];
nr type resnr residue atom cgnr charge mass
typeB
chargeB massB 1 opls_164 1 FLU1 F 0
-0.206 18.99840 2 opls_164
1
FLU1 F 0 -0.206 18.99840
[
bonds ]; ai aj funct 1 2 1 ; F F[ pairs ];
ai
aj funct[ angles ]; ai aj ak funct[ dihedrals ]; ai aj
ak
al funct*
On command gmx grompp -f em.mdp -c alz_F.gro -p alz.top -o ions.tpr
i
get
the following errors
*ERROR 1 [file fluorine.itp, line 21]: No default Bond types*
*NOTE 1 [file alz.top, line 5915]: System has non-zero total charge:
-23.600000 Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>
for
discussion on how close it should be to an integer.*
*WARNING 1 [file alz.top, line 5915]: 16639 non-matching atom names
atom
names from alz.top will be used atom names from alz_F.gro will be
ignored*
Indeed there are only 628 atoms in .top file.
Any suggestions?
--
*Regards,*
*Rahul *
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
[email protected] | (540) 231-3129
http://www.thelemkullab.com
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*Regards,*
*Rahul *
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
[email protected] | (540) 231-3129
http://www.thelemkullab.com
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