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Joined: Oct 2019
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vht Offline OP
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Joined: Oct 2019
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Hi all,

I am using the same umbrella sampling script in the test case and I have few question regarding on that and I would like to clarify them first.

I am considering the reaction coordinate as the distance between the two atoms.

rxncor: umbrella kumb 15.0 form 1 del0 -0.4
rxncor: statistics lowdelta -0.6 hidelta -0.4 deldel 0.002 -
start 500

With regard to above command, if I am correct ,

1). del0 is the initial distance between the specified two points and is it negetive or it is just a dash?.

2). Since the potential is applied between the lowdelta and hidelta. What refers to low and hidelta?. Just in case if I need to maintain the reaction distance in between the 3.3 and 2.5 obviously the delo is 3.5 and then can't I take the lowdelta as 3.5 and also Do I need to specify the minus symbol as well? If so why is it??.

Thanks

Joined: Sep 2003
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please consult doc/umbrel.info for more details

1. del0 is the center of the harmonic bias potential. it should not be negative.
2. the stat subcommand specifies how statistics should be collected during the simulation. it does not affect the potential. the hyphen at the end of the line signals that the command continues on the next line.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  BRBrooks, lennart, rmv 

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