Dear Sir ,
(Bill Ross)
>Try it and see - allow big clearance since density will be low
>since the molecule will be placed in a grid rather than be packed
I have done this and last step of equilibration gives this:
NSTEP =�� 100000�� TIME(PS)
=���� 250.000� TEMP(K) =��
299.31� PRESS =��� 59.6
�Etot�� =����� 6178.0066�
EKtot�� =����� 3863.0849�
EPtot����� =�����
2314.9217
�BOND�� =������
674.1848� ANGLE�� =�����
1878.4011� DIHED�����
=������ 425.5195
�1-4 NB =������ 189.5570� 1-4
EEL =����� 4010.5437�
VDWAALS��� =���� -4097.2245
�EELEC� =����� -766.0599�
EHBOND� =��������
0.0000� RESTRAINT�
=�������� 0.0000
�EKCMT� =������ 685.0976�
VIRIAL� =������ 563.0999�
VOLUME���� =���� 94823.4042
���������������������������������������������������
Density���
=�������� 1.2380
�Ewald error estimate:�� 0.1530E-03
what conclusion can we draw from output regarding density (low or high); please suggest .
At equilibrium, the density vs time plot gives approx. constant
density. Is it sufficiently suggesting that I can use single molecule
as a solvent..
thanks and regards;
JIomm
--- On Mon, 11/16/09, Bill Ross <ross.cgl.ucsf.edu> wrote:
From: Bill Ross <ross.cgl.ucsf.edu>
Subject: Re: [AMBER] slope {no reply}
To: amber.ambermd.org
Date: Monday, November 16, 2009, 5:48 PM
> 2) same query as before.. can we solubilize the system with single molecule
> instead of box solvent
Try it and see - allow big clearance since density will be low
since the molecule will be placed in a grid rather than be packed.
Bill
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Received on Mon Nov 16 2009 - 21:30:03 PST
