[gmx-users] gmx insert-molecules

[Dave Michael]

Thanks, Justin.
I followed "Energy minimization" in
http://md.chem.rug.nl/%7Emdcourse/md.html (pre-running with
http://md.chem.rug.nl/%7Emdcourse/minim.mdp) and it worked just fine.

Dave


On Mon, Jul 11, 2016 at 3:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/11/16 8:38 AM, Dave Michael wrote:
>
>> As I said, I've got limited experience in the chemical/physical aspects of
>> system/topology etc. and I just want some performance indexes
>>
>> Did I make a mistake in the insert-molecules?
>> The online documentation (
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>> )
>> suggests the energy minimization is the next step but I don't know how to
>> do it, can you guide me in the right direction?
>>
>>
> There are lots of GROMACS tutorials available (
> http://www.gromacs.org/Documentation/Tutorials) though CG systems tend to
> work a bit differently.  Since you're starting with MARTINI water systems,
> look into their tutorials (http://md.chem.rug.nl/index.php/tutorials)
> which should provide all the inputs and things you need.
>
> -Justin
>
> Dave
>>
>> On Mon, Jul 11, 2016 at 3:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/11/16 8:15 AM, Dave Michael wrote:
>>>
>>> Hi guys,
>>>>
>>>> I've got a system of 400 water molecules (
>>>> http://md.chem.rug.nl/index.php/example-applications2/solvent-systems)
>>>> and
>>>> I want to make and simulate a system with 1k, 10k, 100k and 1M
>>>> particles.
>>>>
>>>> So far, I've done:
>>>> gmx insert-molecules -ci water.gro -o water.gro -box 4.59151 -nmol 400
>>>> -radius 0.05
>>>> (what I've tried doing is double the box volume and double the number of
>>>> particles and it didn't work without -radius 0.05 / default radius
>>>> doesn't
>>>> add new molecules to the system)
>>>>
>>>>
>>> Probably because insert-molecules doesn't understand whatever the
>>> particle
>>> type is that it's being provided unless you tell it.  CG types are often
>>> not anything like normal atoms.
>>>
>>> And I got a file with 800 particles, some of them have negative
>>> coordinates
>>>
>>>> (I presume those are initial coordinates) and no initial velocities.
>>>>
>>>>
>>>> There are no velocities because insert-molecules doesn't serve that
>>> function, nor would any velocities be meaningful or useful in any way at
>>> this stage.
>>>
>>> Running (GROMACS 5.1.2) md on that file doesn't work as the simulation
>>>
>>>> hangs @ step 0. Using gmx energy I can see that the total energy and
>>>> temperature are off the scales but the density is fine (990 kg/m^3)
>>>>
>>>>
>>>> This suggests something is topologically incorrect.  Have you done
>>> energy
>>> minimization?
>>>
>>> -Justin
>>>
>>> I don't have much experience in the chemical / physical aspects, can you
>>>
>>>> please tell me (step by step if possible) what I missed and what should
>>>> I
>>>> do next?
>>>>
>>>> Dave
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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>>> Gromacs Users mailing list
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
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