Dear Elvis Martis
Thank you very much!
But I still don't konw how to solve this problem because this Error exist in the first step of run minimization and the second step of run heating MD.
I also have check my npt out file, the density of my system is about 0.87, which is agreet with my solvent toluene.
Best wishes!
At 2017-03-06 19:22:26, "Elvis Martis" <elvis.martis.bcp.edu.in> wrote:
> According to AMBER Tutorial B0 ,I first run minimization for my system, then heating MD and finally production MD (npt ,then nvt).
> only run minimization and heating MD with sander.MPI existing "System must be very inhomogeneous" errors, and the end of the production MD can be normal.
>>>> I am clear what do you mean by "can be normal"?
> Another question: the end of all steps can be normal if run MD simulation with pmemd.MPI.
> I am clear what do you mean by "can be normal"?
> Error information are as following:
> >***** Processor 7
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>> In this slab, Atoms found: 580 Allocated: 531
>>
>>
>>***** Processor 9
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>> In this slab, Atoms found: 540 Allocated: 531
>>
>>
>>***** Processor 7
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>
>> In this slab, Atoms found: 532 Allocated: 531
>My input files are:
>For run minization:
> Initial minimisation(MM)
> &cntrl
> imin=1, maxcyc=16000, ncyc=4000,
> ntf=1, ntc=1,
> cut=8.0, ntb=2, ntp=1
> /
> For heat MD :
>Heat 100 ps MD temp:0-300(MM)
> &cntrl
> imin=0,ntx=1,irest=0,
> ntf=2, ntc=2, ntp=0,
> cut=8.0, ntb=1,
> tempi=0.0, temp0=300,
> nstlim=100000, dt=0.001 ,
> ntpr=1000, ntwx=1000,ntwr = 1000,
> ntt=3,gamma_ln=2.0,
> nmropt=1,ig=-1
> /
>&wttype='TEMP0',istep1=0,istep2=85000,value1=0.0,value2=300 /
>&wttype='TEMP0',istep1=85001,istep2=100000,value1=300,value2=300 / &wt type='END' /
>
>I guess there are regions of vacuum in your system.
>Have you looked at your density equilibration outfile??
>Maybe it could give you some hints
>
> Best Regards
>
>
>
>Elvis Martis
>Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
>A Kalina, Santacruz [E], Mumbai 400098, INDIA
>W www.elvismartis.in
>Skype. adrian_elvis12
>
>
>
>
>-----Original Message-----
>From: 杨满意 [mailto:ymy0664.163.com]
>Sent: Monday, March 06, 2017 4:24 PM
>To: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Amber 16 MD simulation Problems
>
>Dear Elvis Martis
> Thanks for your reply !
> MY problem is :
> According to AMBER Tutorial B0 ,I first run minimization for my system, then heating MD and finally production MD (npt ,then nvt).
> only run minimization and heating MD with sander.MPI existing "System must be very inhomogeneous" errors, and the end of the production MD can be normal.
>>>> I am clear what do you mean by "can be normal"?
> Another question: the end of all steps can be normal if run MD simulation with pmemd.MPI.
> I am clear what do you mean by "can be normal"?
> Error information are as following:
> >***** Processor 7
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>> In this slab, Atoms found: 580 Allocated: 531
>>
>>
>>***** Processor 9
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>> In this slab, Atoms found: 540 Allocated: 531
>>
>>
>>***** Processor 7
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>
>> In this slab, Atoms found: 532 Allocated: 531
>My input files are:
>For run minization:
> Initial minimisation(MM)
> &cntrl
> imin=1, maxcyc=16000, ncyc=4000,
> ntf=1, ntc=1,
> cut=8.0, ntb=2, ntp=1
> /
> For heat MD :
>Heat 100 ps MD temp:0-300(MM)
> &cntrl
> imin=0,ntx=1,irest=0,
> ntf=2, ntc=2, ntp=0,
> cut=8.0, ntb=1,
> tempi=0.0, temp0=300,
> nstlim=100000, dt=0.001 ,
> ntpr=1000, ntwx=1000,ntwr = 1000,
> ntt=3,gamma_ln=2.0,
> nmropt=1,ig=-1
> /
>&wttype='TEMP0',istep1=0,istep2=85000,value1=0.0,value2=300 /
>&wttype='TEMP0',istep1=85001,istep2=100000,value1=300,value2=300 / &wt type='END' /
>
>
>
>
>
>
>
>
>
>
>
>
>
>At 2017-03-05 18:28:54, "Elvis Martis" <elvis.martis.bcp.edu.in> wrote:
>>HI,
>>Does your simulation crash?? Can you tell us little more about your system?
>>There are similar posts on this
>>http://archive.ambermd.org/201108/0444.html
>>http://archive.ambermd.org/201209/0040.html
>>
>> Best Regards
>>
>>
>>
>>Elvis Martis
>>Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy
>>
>>
>>A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in
>>Skype. adrian_elvis12
>>
>>
>>
>>
>>-----Original Message-----
>>From: 杨满意 [mailto:ymy0664.163.com]
>>Sent: Sunday, March 05, 2017 9:41 AM
>>To: amber.ambermd.org
>>Subject: [AMBER] Amber 16 MD simulation Problems
>>
>>Hi,
>> when I us amber 16 to do simulation, I always have the following
>>probems
>>
>>
>>***** Processor 7
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>> In this slab, Atoms found: 580 Allocated: 531
>>
>>
>>***** Processor 9
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>> In this slab, Atoms found: 540 Allocated: 531
>>
>>
>>***** Processor 7
>>***** System must be very inhomogeneous.
>>***** Readjusting recip sizes.
>> In this slab, Atoms found: 532 Allocated: 531
>>
>>
>>
>>
>>My inputfile:
>> Heat 100 ps MD temp:0-300(MM)
>> &cntrl
>> imin=0,ntx=1,irest=0,
>> ntf=2, ntc=2, ntp=0,
>> cut=8.0, ntb=1,
>> tempi=0.0, temp0=300,
>> nstlim=100000, dt=0.001 ,
>> ntpr=1000, ntwx=1000,ntwr = 1000,
>> ntt=3,gamma_ln=2.0,
>> nmropt=1,ig=-1
>> /
>>&wttype='TEMP0',istep1=0,istep2=85000,value1=0.0,value2=300 /
>>&wttype='TEMP0',istep1=85001,istep2=100000,value1=300,value2=300 / &wt
>>type='END' /
>>
>>
>>
>>
>>How can I solve these problems. Thanks!
>>
>>
>>_______________________________________________
>>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
>_______________________________________________
>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 Mon Mar 06 2017 - 04:00:02 PST
