Have you any suggestions?
2013/1/15 Elisa Frezza <elisa.frezza.gmail.com>
> Dear Adrian,
>
> thank you very much for your answer. I am using AMBER12 and I am not sure
> that I can use COM restraint.
> At the same time, if I use only a distance restraint, my molecules start
> to rotate and they are not parallel each other.
>
> In conclusion, my question is: Can I put a lot of restraints and then
> consider only a distance between two atoms or is it not right?
>
> Elisa
>
>
> 2013/1/15 Adrian Roitberg <roitberg.ufl.edu>
>
>> Elisa,
>> Look at the Center of Mass restraints in the manual.
>>
>> Also, if you want distance and angle PMF, you would need at least a 2-D
>> umbrella sampling scheme.
>>
>> adrian
>>
>> On 1/15/13 9:12 AM, Elisa Frezza wrote:
>> > Dear All,
>> >
>> > I am doing Umbrella Sampling on a pair of dodecamer and I would like to
>> > obtain the PMF as a function of the relative distance and orientation.
>> > I have noticed that I have to use a lot of restrains.
>> > My question is:
>> > is it right to put the restraint for each bond? Is it right to obtain
>> the
>> > PMF?
>> >
>> > My restraint files is like this:
>> >
>> >
>> > #DNA
>> > #dna
>> > &rst
>> > iat=62,820
>> > r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
>> > &end
>> > &rst
>> > iat=92,850
>> > r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
>> > &end
>> > &rst
>> > iat=125,883
>> > r1=0.0000E+00,r2=28.0000,r3=28.0000,r4=56.000,rk2=5,rk3=5,ir6=0,
>> > &end
>> >
>> > ......
>> >
>> > thank you in advance
>> >
>> > Elisa
>> >
>>
>> --
>> Dr. Adrian E. Roitberg
>> Professor
>> Quantum Theory Project, Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>>
>>
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>>
>
>
>
> --
> Elisa Frezza
> Ph.D. Student in Materials Science and Engineering
> Dipartimento di Scienze Chimiche
> Università di Padova
> via Marzolo, 1
> 35131 Padova - Italy
> Phone: +39 049 827 5149
> Skype: elisa.frezza
> Emai: elisa.frezza.gmail.com
> elisa.frezza.studenti.unipd.it
>
>
>
--
Elisa Frezza
Ph.D. Student in Materials Science and Engineering
Dipartimento di Scienze Chimiche
Università di Padova
via Marzolo, 1
35131 Padova - Italy
Phone: +39 049 827 5149
Skype: elisa.frezza
Emai: elisa.frezza.gmail.com
elisa.frezza.studenti.unipd.it
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Received on Tue Jan 15 2013 - 07:30:04 PST
