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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 15 2010 - 22:30:02 PDT
