[gmx-users] high temperature

[mah maz]

Hi Justin,
That's the .mdp file.
dt                  =  0.0001
tinit               =  0
nsteps              =  100000
nstxout             =  1000
nstvout             =  1000
nstfout             =  0
nstlog              =  1000
nstenergy           =  1000
nstlist             =  5
ns_type             =  grid
rlist               =  0.2
coulombtype      = reaction-field-zero
epsilon_rf =         0
rcoulomb            = 0.1
rvdw                =  0.2
vdwtype             =  cutoff
pbc                 = no
integrator          = md-vv
Tcoupl              =  nose-hoover
tau_t               =  0.1 0.1
ref_t               =  300 300
tc_grps             = CNT water

unwanted temperatures from the 2nd computer are:

0.000000
569.41912
487.04663
428.94406
548.68127
406.10748
533.70324
487.37088
456.60519
452.93588
442.06088
463.36178
472.95275
502.68411
421.56173
492.36709
537.82879
483.68277
475.07675
494.39749
452.90744
494.20474
474.09298
482.93124
487.88989
509.66070
454.61138
453.75927
460.47540
454.69632
505.48443
485.54705
472.73492
460.27398
493.66903
480.78952
482.55233
470.91381
496.23098
484.82730
455.13006
469.39798
506.39819
479.32211
500.88891
485.77325
489.26815
476.03207
469.77734
466.56793
493.62396
482.78839
470.33157
462.17074
477.09906
470.76757
489.31381
486.11468
475.64276
471.49072
482.00595
485.38873
480.53643
475.79977
469.22253
488.72970
481.01446
493.13934
486.96911
481.62371
469.96023
488.82580
482.96316
476.70632
487.02590
487.53659
476.29904
472.44818
479.97314
477.46865
473.29275
469.93447
474.75863
472.98861
478.05273
486.17233
480.43383
475.78836
482.39563
480.41461
476.73916
490.22122
482.99255
478.54370
480.67889
478.16925
479.58938
474.47232
484.70156
484.90008
481.15057
---------------------------------
wanted temperatures from the 1st computer:

0.000000
326.691895
294.764709
298.554596
282.649414
307.463135
291.600189
300.543671
299.999359
297.054443
305.510986
303.078583
299.970428
299.137207
297.810272
298.365875
298.783813
301.805695
303.370575
300.340332
301.656372
299.389984
300.836243
296.977936
298.827637
299.861847
300.578522
296.483398
296.462646
302.666473
297.978180
304.715515
300.773193
300.172913
307.178711
298.444183
312.749542
302.172089
301.957428
303.820526
303.579712
296.149872
296.983826
303.023834
299.992371
299.144897
295.766663
305.296722
304.449219
309.249756
302.303375
304.800293
301.949646
302.895538
307.148254
298.277069
302.761719
296.531281
296.709900
298.417542
300.391022
297.293732
299.136353
290.259125
299.269531
305.229675
301.938751
301.106384
301.689117
295.249969
298.655914
296.441071
300.491364
304.039795
301.149384
295.906250
300.652557
296.303467
300.960083
304.725067
291.927765
303.753845
300.202393
294.915588
297.580017
302.882233
300.872406
306.164551
299.459473
300.940948
306.348328
299.031982
299.465942
297.603119
301.168304
305.233917
292.175751
304.453491
300.391571
303.061188
302.262146
Hope they are the data you wanted.
Thanks for your time and help.

On Tue, Mar 3, 2015 at 10:30 PM, mah maz <mahmaz71 at gmail.com> wrote:

> 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>