*This is the input file. NMR restraints are commented out:*
&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=8,
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
#DIPOLE=RST.dip
#DISAND=paraFE.dist
&end
*This is the job script:*
#$ -l tp
#$ -q tp.q
#$ -pe orte 12
#$ -N MycGMIV
#$ -cwd
#$ -V
cd $SGE_O_WORKDIR
module load AMBER/14
### for a serial job
### sander -i yourinput.in etc etc etc
### for a parallel job
mpirun -np $NSLOTS `which sander.MPI` -O -i test.in -o test.out -p
MycGMIVparm.prmtop -c MycGMIVrestart_file.rst -r MycGMIVtest.rst -x
MycGMIVtest.mdcrd
*Head of .rst file**:*
73050 0.2721000E+04
57.5838040 11.4653584 58.1855211 57.9645901 10.5980577 58.5360797
56.8201328 11.6248323 58.8269904 58.2551780 12.2199049 58.1896656
*Tail:*
0.0313899 -0.3047670 -0.1482668 -0.1407586 -0.4972181 -0.5943622
-2.0873540 -0.3791400 -1.0060945 0.2455087 0.0837746 0.0843920
0.2213739 -0.6646161 -0.2098211 0.3763265 0.0511313 0.7152435
94.6698719 90.1052711 85.7499074 90.0000000 90.0000000 90.0000000
On 5/17/16 3:37 PM, Carlos Simmerling wrote:
> it might help if you post the mdin and script that generated this output.
> also include the head and tail of the restart file, if that was the inpcrd.
>
> On Tue, May 17, 2016 at 3:27 PM, Thomas Pochapsky <pochapsk.brandeis.edu>
> wrote:
>
>> 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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>>>>
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>>
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Received on Tue May 17 2016 - 13:30:04 PDT
