[gmx-users] high temperature

[Justin Lemkul]

On 3/2/15 10:33 AM, mah maz wrote:
> Dear Justin,
> Thank you very much for your answer. Cutoffs are not set by exact studies
> and as you said they are arbitrary. Actually I don't know how to choose
> them for my system. I have CNT in water not vacuo. I tried
> rvdw=rcoulomb=rlist=0 but temperatures are still high. I studied the manual
> but don't know how to set them. Have you got any ideas to help?

If you have a CNT in water, you have several serious problems.

1. The cutoffs.  You need to know what values are used in the force field 
parametrization.

2. A plain cutoff for electrostatics will lead to massive artifacts and heating. 
  I suspect this is a main contributor to your problem.

3. Your tc-grps only specify the CNT, which means the water is not coupled to a 
thermostat!  Coupled with the cutoff artifacts, your water is just accumulating 
heat.

Study some basic tutorials for fundamental "normal" settings.

-Justin

> thanks!
> Cheers
>
> On Sun, Mar 1, 2015 at 8:55 PM, mah maz <mahmaz71 at gmail.com> wrote:
>
>> Dear Chaban,
>>
>> Thank you very much. Could you please explain more about the problem and
>> how I may fix it?
>>
>> Cheers
>>
>> On Sun, Mar 1, 2015 at 11:16 AM, mah maz <mahmaz71 at gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> I have a CNT system. I have set the mdp file as follows, but the
>>> temperature output is logically more than what I expected even in the
>>> production step(around 500k). I have changed the mdp file several times but
>>> it doesn't work. What are the possible causes of problem?
>>> Thank you!
>>> dt                  =  0.0001
>>> tinit               =  0
>>> nsteps              =  2000000
>>> nstxout             =  1000
>>> nstvout             =  1000
>>> nstfout             =  0
>>> nstlog              =  1000
>>> nstenergy           =  1000
>>> nstlist             =  5
>>> ns_type             =  grid
>>> rlist               =  0.9
>>> coulombtype         =  cut-off
>>> rcoulomb            = 0.9
>>> rvdw                =  0.9
>>> rvdw_switch         =  0.5
>>> vdwtype             =  switch
>>> pbc                 = no
>>> integrator          = md-vv
>>> Tcoupl              =  nose-hoover
>>> tau_t               =  0.1
>>> ref_t               =  300
>>> tc_grps             = CNT
>>> gen_temp            = 300
>>> pcoupl               = no
>>>
>>>
>>

-- 
==================================================

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

==================================================