[gmx-users] spurious forces while doing pulling simulation

[Amit Choubey]

Hi,

I am still not able to see the reason for the periodic distances coming into
picture.

Also, why pull_geometry = direction_periodic cannot be used with P-coupling;
although it seems to do what i want.

Amit

On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey <kgp.amit at gmail.com> wrote:

> Hi,
>
> Initially, the pull group center of mass is at 8.16 nm and i want to pull
> 15 nm. I started with a box size of 37 nm in the pull direction.
>
> The problem occurs when the COM is at 18.5 nm (ie at half the box length).
>
> Thanks for the attention.
>
> Amit
>
> On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul <jalemkul at vt.edu>wrote:
>
>>
>>
>> Amit Choubey wrote:
>>
>>> Hi all,
>>>
>>> I am trying to do pulling simulation. Following are the pull parameters
>>>
>>> pull = umbrella
>>> pull_geometry = direction
>>> pull_vec1 = 0 0 1
>>> pull_group1 = RNA
>>> pull_rate1 = 0.01
>>> pull_k1 = 1000
>>> pull_start = yes
>>>
>>> Everything works fine until the pull group COM reaches half the box
>>> length. The COM position changes by the box length and that causes huge
>>> force on the group. What should i do to fix this ? Also i am using NPT
>>> coupling.
>>>
>>>
>> You have to use a sufficiently large box, otherwise the periodic distance
>> becomes the reference distance when this happens.  This has been discussed
>> numerous times on the list (hint: there is an archive for a reason!) and in
>> the tutorial linked here:
>>
>>
>> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>>
>> -Justin
>>
>>  Amit
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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