On 7/27/15 10:35 AM, Daniele Veclani wrote:
OK! I got it
I created the topology with automated topology builder, and I also
optimized the
molecule in gaussian, and the charges are similar.
Are there other ways to derive the cherges?
GROMOS force fields are very empirical. The charge deriv
OK! I got it
I created the topology with automated topology builder, and I also
optimized the
molecule in gaussian, and the charges are similar.
Are there other ways to derive the cherges?
D.V.
2015-07-27 16:30 GMT+02:00 Justin Lemkul :
>
>
> On 7/27/15 10:28 AM, Daniele Veclani wrote:
>
>> Ye
On 7/27/15 10:28 AM, Daniele Veclani wrote:
Yes I have a experimental value.
DGexp=1.99 kcal/mol
DGcalc.=-14.36 kcal/mol
But if I stop the VdW transformation, i get:
DGonlyVdW= 2.38 and this value is in line with other data found in the
literature.
That's only part of the transformation.
On 7/27/15 10:20 AM, Hannes Loeffler wrote:
What happens when you do both transformations simultaneously, i.e.
sc-coul=yes?
That's not a simultaneous transformation of Coulomb terms, rather sc-coul
applies a soft-core to the Coulomb interactions. Actually turning off vdW and
Coulomb simul
Yes I have a experimental value.
DGexp=1.99 kcal/mol
DGcalc.=-14.36 kcal/mol
But if I stop the VdW transformation, i get:
DGonlyVdW= 2.38 and this value is in line with other data found in the
literature.
Thank you for your answer
D.V.
2015-07-27 16:08 GMT+02:00 Justin Lemkul :
>
>
> On 7/27/
What happens when you do both transformations simultaneously, i.e.
sc-coul=yes?
On Mon, 27 Jul 2015 15:55:04 +0200
Daniele Veclani wrote:
> I'm trying to calculate the solvation free energy of a molecule (M).
>
> I have done a VdW. transformation.
>
> I have done also a electrostatic trans
On 7/27/15 9:55 AM, Daniele Veclani wrote:
I'm trying to calculate the solvation free energy of a molecule (M).
I have done a VdW. transformation.
I have done also a electrostatic transformation. But I get an incorrect
value (large overestimation of DG solvation).
So presumably you have
I'm trying to calculate the solvation free energy of a molecule (M).
I have done a VdW. transformation.
I have done also a electrostatic transformation. But I get an incorrect
value (large overestimation of DG solvation).
I use gromacs 5.0.4 with gromos 54a7 force fields and my .mdp file (for
