Hi,
Dear gromacs users,
I am trying to use FEP method for the calculation of relative binding free
energy of peptide-protein complex. I am using gmx-3.3.1.
As per previous discussions on the mailing list, i learnt that i need to
do two different sets of simulations for my case. first set will be for
modification of electrostatics and second one for vdw. The second set
should be started with a structure from the last simulation of first set.
And every simulation in each set should be run independent of each other
with em and water-equilibration at each lambda value.
following are the values for peptide only (not in complex) simulation in
SPC216 water-box...
lambda dg/dl (avg) error
0.0 55.777174 0.586923
0.015 57.524631 0.808737
0.03 54.648669 1.03151
0.05 54.833890 1.08532
0.1 52.990600 1.70822
0.2 50.377182 1.74758
0.35 46.725657 0.683906
0.5 37.016530 0.826907
0.65 33.239827 2.03776
0.75 27.867797 0.300761
0.85 15.989920 1.66024
0.9 1.591218 0.924152
0.95 -32.877432 1.58611
0.99 -259.656906 9.28882
I assume this is for a calculation where you're inserting/deleting one
or more particles? Are you using soft core? This sort of behavior is
typical when you're doing insertion/deletion without soft core (I
would expect the problem to be near lambda=1 if you are doing deletion
without soft core).
You can of course also have similar problems if you are using soft
core but are using non-ideal parameters for soft core (i.e. the soft
core parameters listed in my tutorial are very carefully chosen).
David
error is calculated by using g_analyze with -ee option
i am getting very huge values at lambda = 1.0. as can be seen from the
values, the steepness of the graph has increased a lot towards end. for
l=1, dg/dl values go till ~ -2 x 10^11.
what can be wrong? I have used the same version of gmx for the
tutorial provided by Dill group. In that case, i am not getting any
problem....
I am completely clueless here... please help..
thanks
bharat
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
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
