[gmx-users] high temperature

[mah maz]

Dear Justin,
You are right, but I'm not asking about conditions in .mdp. I wanted to ask
how a result(of temperature here) can be different from one computer to
another while I have even the same GROMACS versions in both? I copied the .
gro .top .mdp .ndx and .ff from the computer I got the good results to
another, but I see about 150K difference in temperature!
Your help is greatly appreciated.
Thanks!

On Tue, Mar 3, 2015 at 10:41 AM, mah maz <mahmaz71 at gmail.com> 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?
> 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
>>>>>
>>>>>
>>>>
>>>
>>
>