Hi All,
Sorry for replying myself. I think I need to put more information. I used binary input and output to keep precision. These calculation were done on Compaq Alphas.
Do you think if I can proceed nmode calculation with specifiying e.g. 1e+00 for drms to avoid the problem described below?
Thanks
Masaki Tomimoto
SGX Inc
This is the input for minimizaion
&cntrl
ntxo = 0,
ntf = 1, ntb = 0,
dielc = 4,
cut = 99999.0, nsnb = 99999999,
scnb = 2.0, scee = 1.2,
imin = 1, maxcyc = 10000000,
ncyc = 0, drms = 0.000001,
dxm = 0.4, ntmin = 0,
&end
&ewald
eedmeth= 5,
&end
This is the input for normal mode
&data
ntx = 0, ibelly = 1,
ntrun = 1, nvect = 0,
drms = 1e+00,
dielc = 4.0, idiel = 0,
scnb = 2.0, scee = 1.2
&end
Belly: let these residues move
RES 1 1
END
.....
RES 255 255
END
-----Original Message-----
From: Masaki Tomimoto
Sent: Friday, May 02, 2003 8:31 AM
To: amber.heimdal.compchem.ucsf.edu
Subject: Question about BELLY NMODE
Hi All,
I have tried nmode with belly option. I tried two different sander minimization with congugate gradient
First I tried to minimize entire protein. The following is the final result
NSTEP ENERGY RMS GMAX NAME NUMBER
32600 9.6945E+01 2.2785E-05 5.1587E-04 CG 2451
Then I tried to nmode with belly option. I got the following message and calculation was terminated
Root-mean-square gradient of input coords is 0.499624056016825
This is greater than the requested maximum: 1.000000000000000E-005
Second I tried to minimize a part of protein with belly option. The following is the final result
NSTEP ENERGY RMS GMAX NAME NUMBER
15286 -6.3325E+01 8.1900E-06 8.0906E-05 C6 3939
However, when I tried to nmode with belly option (specified the same area as minization), I got the following message
Root-mean-square gradient of input coords is 0.564739523502935
This is greater than the requested maximum: 1.000000000000000E-005
Do you have any idea why? Sander minization and following nmode works only for entire protein, doesn't it? If one want to do nmode with belly option, minimization should be also done in nmode?
Thanks
Masaki Tomimoto
SGX Inc.
Received on Fri May 02 2003 - 16:53:01 PDT
