Thanks, Dave. Meanwhile, we are trying to optimize the alignment
tensors for two sets of RDCs in an explicitly solvated protein using
Amber 14. The .prmtop and .rst files we are using have worked fine for
heating (at constant V) and equilibration (first constant V, then
constant P) runs. When I add the RST.dip file, and hold the structure
constant (freezemol=.true.), I get a sander bomb message:
| Local SIZE OF NONBOND LIST = 11423363
| TOTAL SIZE OF NONBOND LIST = 89068726
SANDER BOMB in subroutine nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander
Here is the input file:
&cntrl
imin=0,
irest=1,
nstlim=10000,
dt=0.002,
ntc=2,
ntx=5,
ntf=2,
nmropt=2,
ntpr=100,
ntwx=500,
iscale=10,
cut=16,
ntb=2,
ntp=1,
tautp=2.0,
igb=0,
ntt=3,
gamma_ln=2.0,
tempi=300.0,
temp0=300.0,
&end
/
&wt type='END' /
LISTOUT=POUT
DISANG=paraFeRestraint.dist
DIPOLE=RST.dip
&end
The last line of the .rst file is:
94.6535997 90.0897835 85.7351683 90.0000000 90.0000000 90.0000000
Where I assume solvent box size is given.
Any suggestions would be appreciated.
Tom Pochapsky
On 6/6/16 1:06 PM, David A Case wrote:
> On Mon, Jun 06, 2016, Thomas Pochapsky wrote:
>
>> If a sander run is stopped by an external event, do I restart the job
>> with -A so as to continue to add to the original .out and .mdcrd files?
> No. The manual says that -A is "mainly" used for replica exchange, but
> I think it should be saying "only" used for replica exchange. (I'm
> counting on someone on ths list correcting me if I am wrong.)
>
> For your situation, you have to manually find the last good restart file,
> and use that (with the -c flag) to begin again, creating new mdout, trj
> and restart files.
>
> ....dac
>
>
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Received on Mon Jun 06 2016 - 10:30:07 PDT
