Note that vdw and electrostatic terms are not used - it's a crude but
useful tool for local cleanup.
Bill
On 6/25/2015 3:35 AM, newamber list wrote:
> Hi David
>
> So the 'relaxation' option in xleap uses the steepest descent or gradient
> algorithm ?
>
> Thanks
> Jiom
>
> On Thu, Jun 25, 2015 at 2:07 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Wed, Jun 24, 2015, newamber list wrote:
>>> I get some errors relieved when I do edit--> relaxation in xleap. I
>> select
>>> some specific residues. Is there something similar possible with mdin
>>> options.
>> Use can use either the ibelly or ntr options (in an mdin file) to minimize
>> just specific residues.
>>
>>> Energy minimization with mdin files does not help me much as I think
>>> minimization does not lead to geometry optimization. Sorry if I have used
>>> terms wrongly.
>> To me, "energy minimization" and "geometry optimization" mean the same
>> thing.
>>
>> ...regards...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 27 2015 - 16:30:03 PDT
