Re: water molecules "collapse" during equilibration

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri May 29 2009 - 17:05:05 CDT

Hi Elia,
could you send me a copy of your topology and input pdb files?
Thanks,
Peter

JC Gumbart wrote:
> Then your psf was somehow improperly generated. I don't know what went
> wrong with autopsf, but as a quick fix, checking the option "regenerate
> angles dihedrals" in the autopsf menu first may help.
>
> Maybe someone more experienced with autopsf can comment?
>
> On May 29, 2009, at 3:49 PM, enz1+@pitt.edu wrote:
>
>>
>>
>> In the .psf file (there are no angle dihedrals at all; neither for water
>> nor protein/lipid here):
>>
>> 57221 WT1 2 TIP3 OH2 OT -0.834000 15.9994 0
>> 57222 WT1 2 TIP3 H1 HT 0.417000 1.0079 0
>> 57223 WT1 2 TIP3 H2 HT 0.417000 1.0079 0
>> 57224 WT1 3 TIP3 OH2 OT -0.834000 15.9994 0
>> 57225 WT1 3 TIP3 H1 HT 0.417000 1.0079 0
>> 57226 WT1 3 TIP3 H2 HT 0.417000 1.0079 0
>> ...
>>
>>
>> and in the parameter file (par_all27_prot_lipid.inp) I used I there was:
>>
>> HT OT HT 55.000 104.5200 ! ALLOW WAT
>> ! TIP3P GEOMETRY, ADM JR.
>>
>>
>> Thanks for your time
>>
>> Elia
>>
>>
>>> I have never used autopsf so I can't say for sure what is happening.
>>> Can you look at the first few lines of your psf file and confirm that
>>> for the water segments, you see auto angles dihedrals?
>>>
>>> Also, you can check the psf file to check if there are angles present
>>> for any water indices.
>>>
>>> On May 29, 2009, at 2:30 PM, enz1+@pitt.edu wrote:
>>>
>>>> The modified topology file (using the GUI Autopsf-generator) is the
>>>> same
>>>> one as top_all27_prot_lipid.inp only with the bond between the H atoms
>>>> deleted.
>>>> Other than that its the same, i.e,
>>>>
>>>>
>>>> RESI TIP3 0.000 ! tip3p water model, generate using noangle
>>>> nodihedral
>>>> GROUP
>>>> ATOM OH2 OT -0.834
>>>> ATOM H1 HT 0.417
>>>> ATOM H2 HT 0.417
>>>> BOND OH2 H1 OH2 H2 ! (last bond needed for shake deleted)
>>>> ANGLE H1 OH2 H2 ! required
>>>> ACCEPTOR OH2
>>>> PATCHING FIRS NONE LAST NONE
>>>>
>>>>
>>>
>>>
>>

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