From: Nassar, Omneya (omnassar_at_UTMB.EDU)
Date: Sun Sep 16 2018 - 22:35:57 CDT
Thank you for answering the question, Peter. That was nice of you and the fast reply was impressive.
On Sep 16, 2018, at 10:23 PM, Haohao Fu <fhh2626_at_gmail.com<mailto:fhh2626_at_gmail.com>> wrote:
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You are correct! Everything seems work when I changed the topology file correspondingly. Thanks for your help!
Peter Freddolino <petefred_at_umich.edu<mailto:petefred_at_umich.edu>> $BP2(B2018$BG/(B9$B7n(B17$BF|<~0l(B $B>e8a(B11:11$B<LF;!'(B
At least one problem is quickly apparent. Quoting the namd manual on the use of the TIP4 water model:
"Specifies the water model to be used. When using the TIP3P water model, the ordering of atoms within each TIP3P water molecule must be oxygen, hydrogen, hydrogen. **When using the TIP4P water model, the ordering of atoms within each TIP4P water molecule must be oxygen, hydrogen, hydrogen, lone pair.**"
Your atom ordering does not obey this rule.
On Sun, Sep 16, 2018 at 9:05 PM, Haohao Fu <fhh2626_at_gmail.com<mailto:fhh2626_at_gmail.com>> wrote:
I'm trying to equilibrate a TIP4P water box using NAMD. However, when I submit such job, the NAMD process will stop in 10 timesteps. I suspect that there are something wrong in my psf file, but I cannot figure out where the problem is.
I used the official version of "toppar_water_ions_tip4p.str" in http://mackerell.umaryland.edu/charmm_ff.shtml Could anyone help me out? Thanks!
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: Tue Dec 31 2019 - 23:20:12 CST
Could anyone help me out? Thanks!
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