[gmx-users] high temperature

[mah maz]

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?
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
>>>>
>>>>
>>>
>>
>