Hello Helena,
I see you are setting saltcon=0.0. Try setting saltcon=0.1.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Aug 24, 2018, at 2:42 AM, Helena Damtoft Tjørnelund <s153842.student.dtu.dk<mailto:s153842.student.dtu.dk>> wrote:
I'm using pmemd.cuda in AMBER 16, but I have also tried with AMBER 18.
Furthermore, if I use the restart files from the last step where the protein is present (frame 498) and restart the simulation, I can get it to run for another 500 steps before the protein disappears again.
BR,
Helena
________________________________
Fra: Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com>>
Sendt: 23. august 2018 16:48:45
Til: AMBER Mailing List
Emne: Re: [AMBER] Problems with constant pH production step
What program are you using?
--
Jason M. Swails
On Aug 23, 2018, at 4:18 AM, Helena Damtoft Tjørnelund <s153842.student.dtu.dk<mailto:s153842.student.dtu.dk>> wrote:
Hello AMBER community,
I am trying to do a constant pH simulation on a protein, but during the production step an error occurs. After 500 steps something goes wrong, as seen below:
wrapping first mol.: 57.92036 81.91175 141.87531
wrapping first mol.: 57.92036 81.91175 141.87531
NSTEP = 400 TIME(PS) = 5001.796 TEMP(K) = 299.67 PRESS = 0.0
Etot = -971786.4313 EKtot = 237328.6719 EPtot = -1209115.1032
BOND = 3999.2974 ANGLE = 10605.4152 DIHED = 14122.9759
1-4 NB = 4762.1390 1-4 EEL = 58004.2211 VDWAALS = 172178.1361
EELEC = -1472787.2880 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
wrapping first mol.: NaN NaN NaN
wrapping first mol.: NaN NaN NaN
NSTEP = 500 TIME(PS) = 5001.996 TEMP(K) = 786.75 PRESS = 0.0
Etot = ************** EKtot = 623078.6875 EPtot = **************
BOND = 26775.7612 ANGLE = 27621.9031 DIHED = 13707.5247
1-4 NB = ************** 1-4 EEL = 57695.9679 VDWAALS = 3252.9726
EELEC = -8428935.9376 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
My input file for the production step is shown below. I have tried different combinations of ntwr, ntpr, and ntwx, but this does not fix the problem - no matter what the error occurs around 500 steps.
Explicit solvent constant pH MD
&cntrl
imin=0, irest=1, ntx=5, ntxo=2,
ntwr=100 ,ntpr=100, ntwx=100, nstlim=1000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=8, iwrap=1,
ioutfm=1, icnstph=2, ntcnstph=500,
solvph=7.5, ntrelax=100, saltcon=0.0,
/
Thank you - Best Regards
Helena Damtoft T.
Technical University of Denmark
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Received on Fri Aug 24 2018 - 02:00:03 PDT
