I'm concerned that your equilibration potential energy is -2914 while during
the exchange it is +3993 kcal. this is a large change. you might want to
check into this- look at the last energy in the equilibration, then for the
very same replica (important!) look at the initial energies in the remd
output. also you should tell us more, such as how you equilibrated each
replica at the right T before starting exchanges.
the other strange thing is that the output you show didn't actually do an
exchange- so it's not likely the REMD part that is the problem. this is
especially true since it's the first exchange, and thus the first MD step. I
suspect that something isn't right with the structure. try to use exactly
the same input file to sander, and change ONLY the remd part. don't do remd,
do standard MD (multi-md, since you have multiple replicas, but they aren't
exchanging) using the same input structures and temperatures, etc. see what
happens. it likely won't work, and MD is easier to sort out than remd. if it
still fails, look carefully at the energies as I mentioned above. you might
want to set ntpr to 1 so you can get more details on the energy.
On Sat, Oct 16, 2010 at 1:02 AM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> Hi Carlos,
>
> Thanks for your reply. I'm glad that someone is going to help me.
> I worked on REMD of the protein at *neutral pH *with following
> equilibration
> input:
> Equilibration
> &cntrl
> irest=0, ntx=1,
> nstlim=1000000, dt=0.002, nrespa=2,
> irest=0, ntt=3, gamma_ln=2.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2,
> ntb=0, igb=5,
> cut=16, rgbmax=16, saltcon=0.2, gbsa=1,
> ntpr=500, ntwx=500, ntwe=500
> /
> &wt TYPE='END'
> /
> DISANG=uhprp_chir.dat
>
> After the equilibration, I worked on REMD with following input:
>
> REMD 2ns
> &cntrl
> irest=1, ntx=5,
> nstlim=1000000, dt=0.002,
> ntt=3, gamma_ln=2.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2, nscm=1000,
> ntb=0, igb=5,
> cut=16, rgbmax=16, saltcon=0.2, gbsa=1,
> ntpr=500, ntwx=500, ntwe=500,
> nmropt=1,
> numexchg=1000,
> /
> &wt TYPE='END'
> /
> DISANG=uhprp_chir.dat
>
> The above inputs worked fine (except that my computer facility can't finish
> 2ns of REMD in one job. I'll resume the job with 0.2ns).
>
> At the same time, I tried to setup REMD with the same protein but at
> *acidic
> * condition. Therefore, I changed ASP, GLU and HIS/HIE to ASH, GLH and
> HIP,
> respectively. I repeat the parameters used for neutral pH to run
> equilibration and REMD. Equilibration was completed as following (adopted
> from one of the mdinfo):
>
> NSTEP = 1000000 TIME(PS) = 2000.000 TEMP(K) = 315.34 PRESS =
> 0.0
> Etot = -846.5296 EKtot = 1347.8953 EPtot =
> -2194.4249
> BOND = 363.4372 ANGLE = 974.8036 DIHED =
> 1190.5679
> 1-4 NB = 374.7025 1-4 EEL = 2904.1595 VDWAALS =
> -569.1035
> EELEC = -5289.7655 EGB = -2202.5385 RESTRAINT =
> 0.0000
> ESURF= 59.3120
>
> ------------------------------------------------------------------------------
> | Current Timing Info
> | -------------------
> | Total steps : 1000000 | Completed : 1000000 | Remaining : 0
> |
> | Average timings for last 500 steps:
> | Elapsed(s) = 38.8 Per Step(ms) = 77.6
> | ns/day = 2.2 seconds/ns = 38813.8
> |
> | Average timings for all steps:
> | Elapsed(s) = 72435.5 Per Step(ms) = 72.4
> | ns/day = 2.4 seconds/ns = 36217.8
> |
> | Estimated time remaining: 0.0 seconds.
>
> ------------------------------------------------------------------------------
>
> After the equilibration, my REMD was stocked with following (adopted from
> one of the mdout):
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> REMD: Initializing remlog.
> REMD: Getting initial energy for replica 1
> | # of SOLUTE degrees of freedom (RNDFP): 4302.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 4302. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> 4302.
> | TOTAL # of degrees of freedom (RNDF) = 4302.
> REMD: Exiting runmd after getting initial energies for replica 1
> REMD: myEptot= 3993.7832 myTargetTemp= 320.00 mytemp= 0.00
> ==========================REMD EXCHANGE
> CALCULATION==========================
> Exch= 1 RREMD= 0
> Replica Temp= 320.00 Indx= 1 Rep#= 1 EPot= 3993.78
> Partner Temp= 370.00 Indx= 24 Rep#= 24 EPot= 4311.51
> Not controlling exchange.
> Rand= 0.184210E+00 MyScaling= -1.00 Success= F
> ========================END REMD EXCHANGE
> CALCULATION========================
> REMD: checking to see if bath T has changed: 320.00->320.00
> | # of SOLUTE degrees of freedom (RNDFP): 4302.
> | # of SOLVENT degrees of freedom (RNDFS): 0.
> | NDFMIN = 4302. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> 4302.
> | TOTAL # of degrees of freedom (RNDF) = 4302.
> vlimit exceeded for step 0; vmax = 20.5344
>
> What shall I do to fix the problem?
> Thanks a lot for the help!
>
> Sophia
>
>
> On Fri, Oct 15, 2010 at 6:55 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > you don't really give us enough information.
> > what do you mean by "on protonated proteins"? how did you build these?
> how
> > was the equilibration done? how long into REMD before it crashed?
> >
> > On Fri, Oct 15, 2010 at 2:24 AM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> >
> > > I had a REMD job running fine with following input:
> > >
> > > REMD
> > > &cntrl
> > > irest=1, ntx=5,
> > > nstlim=1000000, dt=0.002,
> > > ntt=3, gamma_ln=2.0,
> > > temp0=320.0, ig=9665,
> > > ntc=2, ntf=2, nscm=1000,
> > > ntb=0, igb=5,
> > > cut=16, rgbmax=16, saltcon=0.2, gbsa=1,
> > > ntpr=500, ntwx=500, ntwe=500,
> > > nmropt=1,
> > > numexchg=1000,
> > > /
> > > &wt TYPE='END'
> > > /
> > > DISANG=uhprp_chir.dat
> > >
> > > With the sme input parameters, but worked on protonated proteins, I got
> > > following problem:
> > >
> > > ========================END REMD EXCHANGE
> > > CALCULATION========================
> > > REMD: checking to see if bath T has changed: 320.00->320.00
> > > | # of SOLUTE degrees of freedom (RNDFP): 4302.
> > > | # of SOLVENT degrees of freedom (RNDFS): 0.
> > > | NDFMIN = 4302. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> > > 4302.
> > > | TOTAL # of degrees of freedom (RNDF) = 4302.
> > > vlimit exceeded for step 0; vmax = 20.5344
> > >
> > > The job stopped for exceeded velocity.
> > > What shall I do to get the problem solved?
> > > Thanks for the help!
> > >
> > > Sophia
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Received on Sun Oct 17 2010 - 05:30:05 PDT
