p11.out min final result:
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -3.0377E+06 8.6575E+08 1.0275E+11 O1 7970
BOND = 6012.4617 ANGLE = 11318.8017 DIHED = 6168.2191
VDWAALS = 6337.3068 EEL = 15718.3504 HBOND = 0.0000
1-4 VDW = 3886.5626 1-4 EEL = -3087124.6088 RESTRAINT = 0.0000
The GMAX looks pretty high.
> *.rst of p11 (small steps) was continued in p11_1
p11_1.out min:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.0347E+06 8.6401E+08 1.0254E+11 O1 7970
BOND = 6012.4617 ANGLE = 11318.8017 DIHED = 6168.2191
VDWAALS = 6337.3069 EEL = 15718.3504 HBOND = 0.0000
1-4 VDW = 3886.5626 1-4 EEL = -3084108.8709 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -3.5867E+07 1.2346E+11 1.4651E+13 H8 7972
BOND = 6012.4371 ANGLE = 11318.7233 DIHED = 6168.2177
VDWAALS = 6337.1698 EEL = 15714.1927 HBOND = 0.0000
1-4 VDW = 3886.5582 1-4 EEL = ************* RESTRAINT = 0.0000
GMAX still high (atom w/ max force on it).
The high 1-4 EEL suggests to me that there are oppositely-charged
atoms near each other, possibly across residue boundaries.
> My system is made up of repeating residues. I have successfully
> simulated systems containing same residues but in less number (say
> 300). But when I tried to simulate large systems containing large
> number of residues, error occured at minimisation step.
How many total atoms? In vacuum? Box is mentioned later..
It's hard to guess whether you are finding a problem with your
residue definition (e.g. charge derivation), or with the program due
to unusual topology.
> I want to say something regarding following error, may be worthless
> to mention here: (please see p11_1.out file)
> Frac coord min, max: -47467159.5535208 47467160.8211625
> The system has extended beyond the extent of the virtual box."
Unusual to have the box too small for minimization.
> when I tried to relax my system in xleap only the whole system
> got converted in to very large bonds and was pointing at one corner of
> xleap visualiser from center xleap like a 'cone'.=20
Leap's minimization is relatively crude, e.g. it doesn't use charge
or vdw info. It's not used much and could be buggy. I only used it
for cleaning up selected atoms' conformation.
I'm afraid I can't suggest much, just that you could try to find the
size at which the system switches from acceptable to problematic
behavior, which could help debugging.
Bill
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Received on Fri Apr 16 2010 - 10:00:06 PDT
