[gmx-users] Secondary structure loss in implicit solvent simulations

Hi I have a question regarding the implicit solvent implementation in GROMACS 4.5.1 (with GPU acceleration). I have been trying to simulate molecules with varying size (PYP with 125 AAs, BBA5 with ~20 AAs, and and Trigger Factor with 432 AAs), but can't seem to be able to maintain the secondary

[gmx-users] Re: Secondary structure loss in implicit solvent simulations

Hi 1) I am using Amber03 forcefield. 2) In most cases Yes, but in others, implicit solvent simulations tend to crash almost immediately (after reporting segmentation fault). 3) It generally takes less than a couple of 100 ps for the loss of the secondary structure. A few times, I even received

[gmx-users] Re: Secondary structure loss in implicit solvent simulations

Hi It's not necessarily GPU-specific, it's implicit solvent-specific. I don't get these problems in explicit solvent simulations on CPU, only in implicit solvent simulations both on GPU as well as CPU. One of the problems that I can think of is unbalanced charges that I would have balanced out