AMBER Archive (2007)

Subject: Re: AMBER: Still puzzled about this virial computation

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Feb 01 2007 - 10:16:51 CST

One additional clarification -
In the mdin snippet shown below, you actually specify a vdw long range
dispersion correction by vdwmeth=1. To turn it off, you would specify
vdwmeth=0. However, turning it on has no effect because of the use_pme=0,
which basically turns off a ton of stuff in ew_force.f in sander.
Regards - Bob
----- Original Message -----
From: "Robert Duke" <rduke_at_email.unc.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, February 01, 2007 10:35 AM
Subject: Re: AMBER: Still puzzled about this virial computation

>A few comments embedded between ==> and <==.
> Regards - Bob
>
> ----- Original Message -----
> From: "David Cerutti" <dcerutti_at_mccammon.ucsd.edu>
> To: <amber_at_scripps.edu>
> Sent: Thursday, February 01, 2007 3:00 AM
> Subject: AMBER: Still puzzled about this virial computation
>
>
>> Hello,
>>
>> Thanks to Rob and Ross for their helpful inputs. I'm still puzzled a
>> bit about some of the computations, though.
>>
>> I am using the following in my run file, but it appears to be ineffective
>> at removing the various long-range corrections (for which I do not yet
>> have an equivalent in my code) from SANDER:
>>
>> &ewald
>> use_pme=0,
>> eedmeth=4,
>> vdwmeth=1,
>> &end
>>
> ==>
> There are no long range corrections here. See below.
> <==

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