Hi Ross,
Thanks for your reply.
I did again the test job with the following steps in amber9, loaded mdcrd in VMD,
but I don't see any strange thing happen at all.
> Can you try setting ntpr=1 and ntwx=1. Then take a look at the mdcrd file
> that is created in something like VMD and see if you can see anything
> strange happening to the structure. If you could also post the mdout file
> it will be easier to try and work out what is going on.
The topology file is made by:
source leaprc.ff02pol.r1
nma = sequence {ACE NME}
solvateoct nma TIP3PBOX 8.0
saveamberparmpol nma nma.top nma.crd
With mdin:
*************************************
Heating to 100 K
&cntrl
imin = 0, ntx = 1,
irest = 0, iwrap = 1,
ntpr = 1, ntwe = 10,
ntwr = 10, ntwx = 1,
ntave = 500,
ntf = 2, ntc = 2, ntb = 2,
cut = 8.0, nsnb = 10,
nstlim = 500, dt = 0.002,
tempi = 5.0, temp0 = 100.0,
ntt = 1, tautp = 1.0,
ntp = 1, pres0 = 1.0, taup = 1.0,
ipol = 1,
/
&ewald
indmeth = 1,
/
*************************************
Then, the last part of mdout says like this.
------------------------------------------------------------------------------
NSTEP = 229 TIME(PS) = 0.458 TEMP(K) = 43.66 PRESS = -3130.7
Etot = -3468.7970 EKtot = 81.5617 EPtot = -3550.3588
BOND = 0.3924 ANGLE = 0.6519 DIHED = 2.8995
1-4 NB = 0.9568 1-4 EEL = -58.8164 VDWAALS = 608.8347
EELEC = -4103.3945 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 67.6928 VIRIAL = 832.7742 VOLUME = 11318.5174
EPOLZ = -1.8831
Dipole convergence: rms = 0.194E-04 iters = 2.00
Density = 0.8275
------------------------------------------------------------------------------
Cutoff list exceeds largest sphere in unit cell!!
Big problems with imaging!!
a,b,c = 24.4937980338375 24.4937980338375
24.4937980338375
alpha,beta,gamma = 109.471219000000 109.471219000000
109.471219000000
cutlist,sphere = 10.0000000000000 9.99955167855377
*****
If you have any idea to fix the problem, please let me know.
Otherwise, I have no choice but to use "solvatebox".
Thanks.
Seongeun
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Oct 31 2007 - 06:07:50 PDT
