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

[Erik Marklund]

Exactly. So now is the time for skillful scripting.

Erik

Nilesh Dhumal skrev 2011-05-20 15.31:
> 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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>


-- 
-----------------------------------------------
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/