[gmx-users] Re: water dimer is gas phase

[Nilesh Dhumal]

I used the same topology file to run 256 water molecules simulation and I
got the proper result (compared with reported one).

 The problem is to visualize the trajectory in VMD since gromacs fails to
write valid pdb files when the coordinates are too large.

Nilesh


On Fri, May 20, 2011 5:22 am, Erik Marklund wrote:
> Justin A. Lemkul skrev 2011-05-19 22.42:
>
>>
>>
>> Vitaly Chaban wrote:
>>
>>>> For vacuum systems, "pbc = no" in conjunction with zero cutoffs is
>>>> correct to obtain a gas-phase system.
>>>
>>>
>>> For reasonably large box, this is the same heck.
>>>
>>>
>>
>> Setting a box size and using "pbc = xyz" precludes the use of infinite
>> cutoffs, which should be the most rigorously correct way to treat this
>> type of system. With PBC, there are long-range effects that should be
>> avoided.
>>
>>> Nilesh: visualize your system, using VMD or ngmx. The behavior of
>>> your molecular cluster during the first ps will provide an answer. Are
>>> you sure that your topology is healthy?
>>>
>>
>> I agree with this.  The system should be going absolutely haywire :)
>>
>>
>> -Justin
>>
>>
> Yes, this is a good test, and the topology should be inspected. However,
> the observed result is expected for this system. A water dimer coupled to a
> thermostat will dissociate eventually (pretty rapidly) at 300 K. The water
> molecules themselves seem intact. The problem with visualization comes
> from the fact that gromacs fails to write valid pdb files when the
> coordinates are too large. I called this a bug on the developer list one
> or two years ago since this generates pdb files that gromacs itself can't
> read, but the other developers didn't catch on. You can postprocess the
> pdb and cap the coordinates so that they're confined to the range that the
> pdb format allows, but note that this will mess up the water moleucles as
> they get very far apart.
>
> Erik
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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