AMBER Archive (2008)

Subject: Re: AMBER: SPCFW problems

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Tue Oct 28 2008 - 12:57:59 CDT

One more question. I expected the angles containing hydrogen to increase but
the bond containing hydrogen to stay constant. Looking the the prmtop files
I see the following.

   Prmtop FlexWat
SPCFW:
   12151 16 7830 838 5410 1138 3595 2681
0 0
   23191 3607 838 1138 2681 42 93 50
29 1
       0 0 0 0 0 0 0 1
24 0
       0
   Prmtop SHAKE water (TIP3P):
   12154 16 11332 838 1911 1138 3595 2681
0 0
   23195 3608 838 1138 2681 43 92 50
29 1
       0 0 0 0 0 0 0 1
24 0
       0

  NATOM, NTYPES, NBONH, MBONA, NTHETH,

  NATOM : total number of atoms
  NTYPES : total number of distinct atom types
  NBONH : number of bonds containing hydrogen
  MBONA : number of bonds not containing hydrogen
  NTHETH : number of angles containing hydrogen

So the number of bonds containing hydrogen are reduced when using SPCFW?

On Tue, Oct 28, 2008 at 11:50 AM, Naser Alijabbari <na3m_at_virginia.edu>wrote:

> Thanks Dr. Case,
> Turning off 'fast SHAKE' stopped the error. I will try the MD part with
> 1fs timestep.
> So I am guessing for SPCFW
>
> - WAT = SPF
>
> - set WAT.1 name 'SPF'
>
> doesn't do anything because I don't see a change in my prmtop file.
>
>
>
> But I think the SPCFW water is used since there is no complaint from these
> commands.
>
> - loadAmberParams frcmod.spcfw
> - set default FlexibleWater on
>
> On Tue, Oct 28, 2008 at 6:49 AM, David A. Case <case_at_biomaps.rutgers.edu
> > wrote:
>
>> On Mon, Oct 27, 2008, Naser Alijabbari wrote:
>>
>> > I am having problems getting the SPCFW water working.
>> > steps in tleap (I have added "?." To keep the file short):
>> >
>> >
>> > Error: A residue defined as a "fast 3-point water"
>> > is not defined by a triangle of three bonds.
>>
>> Try setting jfastw=4. Of course, this should not be necessary, since you
>> didn't ask for SHAKE anyway. But the code calls a setup routine for
>> SHAKE,
>> even when SHAKE has not been invoked :-(
>>
>> And, check the calculations carefully. As you can tell, not many Amber
>> calculations have actually been done with flexible waters. You may need
>> quite
>> a short time step to get good results.
>>
>> ...dac
>>
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>
>

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