[gmx-users] high temperature

[Justin Lemkul]

On 3/3/15 2:27 PM, mah maz 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

These cutoffs are total nonsense; they are much too short to be physically useful.

> vdwtype             =  cutoff
> pbc                 = no

No PBC in a solvated system?  Is this a droplet or is it supposed to be 
condensed phase?

> 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:
>

Likely garbage from a physically unreasonable setup.  Note that if your 
temperature is zero at time zero, you're not generating velocities, so you're 
then letting Nose-Hoover (which oscillates widely) try to make up a huge 
difference in temperature.  Very unlikely to succeed.

-Justin

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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================