Hello, I have successfully completed the KALP-15 in DPPC membrane tutorial recently and have since moved on to setting up my own protein-membrane system.
For my system I am using POPC lipid parameters with GROMOS 53a6 ff obtained from the Lipidbook (2010 Poger and Mark version). After solvating my system, water flooded the hydrophobic core within the POPC lipid bilayer. I have modified the vdw for the carbon atoms by increasing from 0.15 to 0.375. However, I don’t want to arbitrarily increase the vdw again without possibly causing artificial voids around my protein. Can someone offer suggestions? Thank you for your help. Best, Iris =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
