Re: NAMD Error

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Jul 17 2018 - 16:32:50 CDT

Oh, I missed the part where this is a minimization - that's not a good
idea. NAMD minimization does not wrap along PBCs, so large minimizations
will almost assuredly fail. I would recommend 200 steps at the most (or at
least I've never built a system so ugly that this doesn't work).

My previous advice would probably only help for dynamics.

On Tue, Jul 17, 2018 at 5:18 PM, Shriya Bansal <bansals10_at_gmail.com> wrote:

> Thank you so much for your response. I have increased the margin and
> pairlistdist, but these changes to the configuration file have
> unfortunately resulted in the same errors.
> I have attached two images of the TIP4P-2005 water box from different
> angles; is there a reason that certain molecules are stretched after
> minimization?
>
>
>
>
>
> Best,
> Shriya Bansal
>
>
> On Jul 17, 2018, at 3:17 PM, Brian Radak <brian.radak_at_gmail.com> wrote:
>
> I frequently encounter similar problems with systems that size - most of
> NAMD's performance heuristics are simply not designed for something small.
>
> You can try increasing the margin (maybe 1 or 2?) or pairlistdist (16?
> 18?). You will probably also have less trouble without temperature control.
>
> In general, I've never seen any stability benefit from heating a system
> slowly versus all at once. There might be good reasons to heat a biopolymer
> from a crystal structure, but for water this is almost certainly a waste of
> time.
>
> HTH,
> BKR
>
> On Tue, Jul 17, 2018 at 3:45 PM, Shriya Bansal <bansals_at_uchicago.edu>
> wrote:
>
>> Hello,
>>
>> I have been attempting to minimize and equilibrate a 38A TIP4P-2005 water
>> box model built through CHARMM using the July 2017 TIP4P-2005 topology from
>> http://mackerell.umaryland.edu/charmm_ff.shtml. The minimization for
>> 2000 steps has resulted in a trajectory file that exhibits no motion of the
>> molecules. When this water box is that equilibrated, the error FATAL
>> ERROR: Low global exclusion count! (5180 vs 5184) System unstable or
>> pairlistdist or cutoff too small is produced. I have also commented out
>> the heat up process and set the temperature to a constant value of 300K in
>> attempt to counter this error. Please let me know potential sources of
>> error within the minimization and equilibration steps.
>>
>> Best,
>> Shriya Bansal
>>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:00 CST