Could it be that you get a substantial hysteresis since you do the
mutation quite fast (non-equilibrium effect, dissipative work, etc.)?
Check the dgdl file and maybe increase the simulation time.
cheers, Jochen
Li Qiang wrote:
Dear all Gmxers,
I am calculating a mutation free energy from L<->A for a five AA
peptides using G96 53a6 force field.
however, my dG_for and dG_rev is quite different.
dG_for(lambda=0.00) = - 9.9 kJ/mol
dG_rev(lambda=1.00) = 1.33 kJ/mol
Is there anything wrong with setting up topologies?
Here is the [atoms] part for morphed atoms. and I attached the full
.top in the attachment.
For L->A:
[ atoms ]
17 CH2 2 LEU CB 6 0
14.027 CH3 0 15.035; qtot 1
18 CH1 2 LEU CG 7 0
13.019 DUM 0 13.019; qtot 1
19 CH3 2 LEU CD1 7 0
15.035 DUM 0 15.035; qtot 1
20 CH3 2 LEU CD2 7 0
15.035 DUM 0 15.035; qtot 1
For A->L :
[ atoms ]
17 CH3 2 ALA CB 6 0
15.035 CH2 0 14.027; qtot 1
60 DUM 6 DUM DUM 24 0 13.019
CH1 0 13.019
61 DUM 6 DUM DUM 24 0 15.035
CH3 0 15.035
62 DUM 6 DUM DUM 24 0 15.035
CH3 0 15.035
thanks for help
LQ
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
