AMBER Archive (2008)

Subject: AMBER: Using mdcrd files to look at minor charge changes

From: Cooper, Matthew (matthew_cooper_at_merck.com)
Date: Thu Apr 03 2008 - 13:45:12 CDT


Hi,
I am calculating free energies of solvation using thermodynamic
integration on amber 7 for a number of small molecules.
Each time I change the charges on these small molecules I need to rerun
the simulations to get the numbers for the free energy calculation.
I would like to use the saved mdcrd files along with a new topology
files to estimate the free energy value since the partial charges
differences should not change motion nor the explicit water positions
all that drastically.
I am fine when I just want to get energies but when I use icfe=1 (along
with a clambda value) to try and get the dv/dl values to output, I get a
core dump.
Can anyone help to shed some light on the problem?
Thanks, Matthew

Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu