[gmx-users] high temperature

[mah maz]

I see. I just don't understand the difference between these results.
Useful as always.
Many thanks!

On Tue, Mar 3, 2015 at 10:57 PM, mah maz <mahmaz71 at gmail.com> wrote:

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