[gmx-users] high temperature

[Justin Lemkul]

On 3/3/15 2:11 AM, mah maz wrote:
> Hi Justin,
> I performed the run with the reaction-field-zero as I said, but when I try
> to simulate it with exactly the same conditions on another computer it
> again gives me high temperatures! I again changed the conditions but it
> didn't work. Have you got any suggestions?

The phrase "changed the conditions" means nothing to anyone who isn't seeing 
what you're doing.  Post a full .mdp file.

-Justin

> Thank you!
>
> On Mon, Mar 2, 2015 at 10:08 PM, mah maz <mahmaz71 at gmail.com> wrote:
>
>> Hi Justin,
>> So many thanks for your help. The problem was solved by changing cutoff to
>> reaction-field-zero and epsilon_rf=0. It just may need some modifications
>> for assigning right rvdw, rcoulomb and rlist. Thanks again!
>> Cheers
>>
>>
>>
>> On Mon, Mar 2, 2015 at 7:03 PM, mah maz <mahmaz71 at gmail.com> 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?
>>> 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

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