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

[Nilesh Dhumal]

I run the same mdp files for glucose in vaccum.

I ma geting the proper results, I can visualize the strucutre properly in
VMD.

If I use same for water why I am not geting proper structure ?

Nilesh

On Fri, May 20, 2011 9:48 am, Erik Marklund wrote:
> 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/
>
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