[gmx-users] high temperature

[mah maz]

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
>>>
>>>
>>
>