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:
WARNING: This email originated from outside of UTMB's email system. Do not click links or open attachments unless you recognize the sender and know the content is safe.
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!
This archive was generated by hypermail 2.1.6
: Sat Dec 07 2019 - 23:20:08 CST
Could anyone help me out? Thanks!
This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:08 CST