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

[Wei Fu]

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

Linda

2004-02-13
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  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) 
  Fax:713-743-8351 
  Email: fuwei at adrik.bchs.uh.edu
  http://adrik.bchs.uh.edu/~fuwei/
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