The error message might indicate a problem with the input coordinate file, which I don't have an android app to view. I believe there is a time field at the beginning, which may be garbled. Check the file format definition on the Amber site.
Bill
-------- Original message --------
From: Vu Truong <vutruong.lsp.gmail.com>
Date:06/13/2014 2:35 PM (GMT-08:00)
To: amber.ambermd.org
Subject: Re: [AMBER] "Invalid start to time: 28..." error
Hi,
Thanks so much for your response. I am a graduate student and really new in
Amber which has brought me much in trouble so far. I found this e-mail list
is very helpful to gain more knowledge.
I'm sorry for lack of information that may waste your time. Below is my
input information and the message in the output file. My system consist of
a CeF3 crystal structure with the water box on top of it. Im using Amber 9
and the code is sander.mpi one.
Here is the input file:
md of water drop on cerium fluoride
&cntrl
dielc =1.0, scee = 1.2,
cut =9.0, nsnb =50, ibelly = 1, bellymask = ":TP4"
ntx = 1, irest = 0, ipol = 0, iwrap = 1,
ntf = 2, ntc = 2, tol = 0.00000010100,
ntb = 1, ntp = 0, temp0 = 298.0, tautp = 3.0, taup =
2.0,
nstlim = 1000, nscm =-1, dt = 0.002, maxcyc = 1000, imin = 0, ntmin = 2,
ntpr =1000, ntwx = 1000, ntt = 3, ntr = 0, a4p=0.106677717,
jfastw = 0, pres0 = 1.0, tempi = 0.0, gamma_ln = 5.0,
&end
&ewald
indmeth=1, diptau=10.1, skinnb=1.0,
&end
And this is the message of error:
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
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 = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 295661
| TOTAL SIZE OF NONBOND LIST = 295661
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -2129124.1117 EKtot = 0.0000 EPtot =
-2129124.1117
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
-2219.8570
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
EELEC = -2126904.2546 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Ewald error estimate: 0.9764E+00
------------------------------------------------------------------------------
Invalid start to time: 28 ▒▒?~Aqq^Y^T▒ ▒▒^X{&{d▒
I'm also sending my topology file and the coordination file which is got
after running minimization as per this dropbox link:
https://www.dropbox.com/sh/650kl1lkl1h35nf/AABbGoGhzD5n4FXjcoCVtsM1a
Besides, I have 1 more question to better get used with the e-mail list. I
usually get an e-mail from Amber-request everyday. How to reply your e-mail
directly from the Amber archive page?Its because I need to wait for a day
to get your responses from Amber-request...
Once again, thanks so much for all your concern.
Best Regards,
Vu T.
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Received on Fri Jun 13 2014 - 18:30:02 PDT
