Dear Amber Users,
I'm trying to carry out a very simple minimization.
For this purpose I'm using the following flags:
Minimization
&cntrl
imin=1, ntr=0,
cut=6, ntpr=100, scee=1.2, drms=0.0001,
maxcyc= 3000, ntmin=1, ncyc=1000, nsnb=25,
dielc = 4.0,
&end
After getting the topology and coord file from xleap,
I try to launch sander8.serial and I got the following errors:
a) If I do not set a box sander start running but do not
print any result while one processor is at 100%.
I've obtained RU5.topology RU5.coord from leaprc.ff99,
just making saveamberparm RU5 or NSER.
b) If I set a box:
setbox NSER centers
,and get the coord and top files the results are:
==> NSER.outm1 <==
Here is the input file:
Minimization
&cntrl
imin=1, ntr=0,
cut=6, ntpr=100, scee=1.2, drms=0.0001,
maxcyc= 3000, ntmin=1, ncyc=1000, nsnb=25,
dielc = 4.0,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 1.511
PARAMETER RANGE CHECKING:
parameter nfft1: (grid size) has value 4
This is outside the legal range
Lower limit: 6 Upper limit: 2048
The limits may be adjustable; search in the .h files
c) So I edit the box dimensions to 16 16 16 and
I got:
[...]
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
Exceeding lastrst in get_stack
lastrst = 11618
top_stk= 0
isize = 21281
request= 21281
Increase lastrst in the &cntrl namelist
I think I would set the box size at least twince the cut off.
If I run this same flags for a big system it runs fine.
How can I run this minimization just for a single residue?.
Thank you,
JJ
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- application/octet-stream attachment: RU5.min1
- application/octet-stream attachment: RU5.outm1
- application/octet-stream attachment: NSER.min1
Received on Wed Feb 14 2007 - 06:07:44 PST
