[gmx-users] gmx insert-molecules

[Dave Michael]

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?

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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