The .prmtop, .crd and .rst files are all "legacy" from (successful? at
least completed) AMBER 11 runs. I am currently trying to run with a set
of RDC restraints, with freezemol=true, to optimize the alignment
tensor. Where do I find the box dimensions?
thanks,
tom p.
On 5/17/16 3:01 PM, Carlos Simmerling wrote:
> how did you generate this input structure? I might be wrong but it looks to
> me that it thinks you have a negative box dimension.
>
> On Tue, May 17, 2016 at 2:45 PM, Thomas Pochapsky <pochapsk.brandeis.edu>
> wrote:
>
>> Dear all,
>>
>> I am taking some .prmtop and .rst files that worked using AMBER 11, but
>> am having trouble with maxing out the NONBOND LIST size in Amber 14.
>> Here is what I am seeing if I cut the nonbonded interactions to 8 Å:
>>
>> | # of SOLUTE degrees of freedom (RNDFP): 149324.
>> | # of SOLVENT degrees of freedom (RNDFS): 0.
>> | NDFMIN = 149324. NUM_NOSHAKE = 0 CORRECTED RNDFP = 149324.
>> | TOTAL # of degrees of freedom (RNDF) = 149324.
>> ---------------------------------------------------
>> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>> using 5000.0 points per unit in tabled values
>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
>> ---------------------------------------------------
>> | Local SIZE OF NONBOND LIST = 15160735
>> | TOTAL SIZE OF NONBOND LIST = 15160735
>> Cutoff list exceeds largest sphere in unit cell!!
>> Big problems with imaging!!
>> a,b,c = -1244.71951386096 -1184.70414062345
>> -1127.43981723746
>> alpha,beta,gamma = 90.0000000000000 90.0000000000000
>> 90.0000000000000
>> cutlist,sphere = 10.0000000000000 -1778.43173586094
>>
>>
>> If I leave the cutoff at 16Å, the program crashes because the non-bonded
>> list is too large. Is there some file that I don't have write access to
>> that stores NBs? This is a solvated simulation. If this is a simple
>> problem, great, if not, I can provide more info upon request.
>>
>> Thanks,
>> Tom Pochapsky
>>
>>
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Received on Tue May 17 2016 - 12:30:04 PDT
