[gmx-users] Ask help about stochastic dynamics at different protonation state

Wei Fu fuwei at adrik.bchs.uh.edu
Fri Feb 13 19:07:01 CET 2004

Hi, all,

  I run SD with hbonds constraint and 2fs timestep by using GROMACS-3.2 in Itanium2 cluster (with 8 CPUs). The problem is that when the simulation goes further (for example, to 100ps), it began to generate "nan" coordinate. I think the reason is that I use GROMOS force field while doing SD, the epsilon_r = 1 could cause trouble for groups which have net charges. I do not choose FF43GB1 because my protein has very different protonation states at PH=4.4 and PH=7, which is responsible for important function of protein. So, first, I calculate the pKa and electrostatic potential by UHBD program (use Monte Carlo algorithm) and found the total charge of protein is around -21 at ph=7, and the total charge is around +3 at PH=4.4. That is, some charged residues like ASP, GLU and HIS have very different protonation state. We just want to compare the dynamics behavior difference at these two states, so I think, the FF43GB1 is not suitable for my study.  On the other hand, the protein undergoes large conformational moti


  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry 
  University of Houston
  4800 Calhoun Rd. HSC #402C
  Houston, TX 77204-5001   USA
  Phone:713-743-8355(o)  713-795-9270(h) 
  Email: fuwei at adrik.bchs.uh.edu

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