[gmx-users] water genbox 3x3x0.8 EM not successful T too high

[Dallas Warren]

Why can't you energy minimise the water block / film in the final box
size?


And you can't simply change the cut-offs like that to suit your box
size, you need to use the settings that the forcefield was parameterised
for, or what others have studied / published and found to be suitable.
You can't swap and changes those settings at a whim.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu

+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of gromacs
Sent: Friday, 17 December 2010 11:32 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T too high

 

 

 


>Message: 3
>Date: Thu, 16 Dec 2010 11:50:51 -0500
>From: Vitaly Chaban <vvchaban at gmail.com>
>Subject: [gmx-users] Re: water genbox 3x3x0.8 EM not successful T not
>           high
>To: gmx-users at gromacs.org
>Cc: gromacs <ptf1242 at 163.com>
>Message-ID:
>
<AANLkTikYKV=-oEV10BxgYs5N_nMqxbonwbHxkybuHJQd at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
> 
>> From: gromacs <ptf1242 at 163.com>
>> Subject: [gmx-users] water genbox 3x3x0.8 EM not successful T not
high
> 
>> Hi,
>> 
>> I want to simulate 3x3x0.8 water film (bulk water) first creat the
water,
>> 
>> genbox -cs -o film.gro -box 3 3 0.8
>> 
>> then, i EM the bulk water;
>> 
>> Using steep, but
>> 
>> t = 0.011 ps: Water molecule starting at atom 298 can not be settled.
>> Check for bad contacts and/or reduce the timestep.
>> Wrote pdb files with previous and current coordinates
>> 
>> 
>> then i run, and i get the result. I use NPT, and T=300K. I run
several times, but the final T was still 411K.
>> 
>> 
>> 
>> So what could i do to get EM process successful?
>> 
>> And what is the reason ? why i can not control the T 300K?
>> 
>> 
>> 
>> Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
>>
------------------------------------------------------------------------
-------
>> Potential                  -9496.38    136.145    135.455  -0.158085
-47.4256
>> Kinetic En.                  2358.2    73.5876    73.5471 -0.0281891
-8.45676
>> Total Energy               -7138.19    136.284    135.326  -0.186274
-55.8824
>> Temperature                 411.945    12.8548    12.8477 -0.00492426
-1.47728
>> Pressure (bar)             -1.66406    704.355    704.355 -0.00424907
-1.27473
>> Box-X                       2.91791  0.0128965  0.0128789 -7.7826e-06
-0.00233479
>> Box-Y                       2.91791  0.0128965  0.0128789 -7.7826e-06
-0.00233479
>> Box-Z                      0.778108 0.00343907 0.00343437
-2.07536e-06 -0.000622609
>> Density (SI)                 1038.7    13.6165    13.5998 0.00778513
2.33555
>> Heat Capacity Cv:        12.49 J/mol K (factor = 0.000973754)
> 
> 
> 
>Hey, gromacs -
> 
>Nice to hear from you here... It is a bad idea to simulate something
>with any cartesian dimension lower than a couple of nanometers using
>classical FFs.  All your problems are generated by 0.8 nm of the
>z-side.
> 
>--
>Dr. Vitaly V. Chaban
>Rochester, U.S.A.
> 
> 
>------------------------------
> 


Thanks very much. I use the cutoff=0.38, because the cutoff should be
smaller than the half box size. I guess it may be the Z dimension is too
small, Plus the PBC. But when i use 1.8x1.8x1.8nm bulk water, all
results are OK.

My teacher wants me to simulate 3x3x0.8, 3x3x0.9 nm water film's
rupture. So i have to run bulk 3x3x0.8 water and then add box to 3x3x9
to form interface.

So if i want to run run bulk 3x3x0.8 water, how could i do? which FF
should i use? the high T may be due to EM not success??



 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101217/aad5ae0a/attachment.html>