Hi,
Maybe you have a look into the nfe (formerly ncsu) code? This is
available in Amber16/pmemd and in the AmberTools16 with sander. Then
there is also plumed2 but sander only at the moment. Either code
allows you to do SMD with a wide range of collective variables, also
multi dimensional.
Cheers,
Hannes.
On Sat, 8 Apr 2017 09:57:26 +0530
Suchetana Gupta <tutulg.gmail.com> wrote:
> Dear Amber users
> I am trying to perform steered molecular dynamics simulation where I
> want to change the distance between two atoms (or better if it is COM
> between a group of atoms) as well as changing the angle between three
> atoms (or COM again). I have used the following input file:
>
> SMD
> &cntrl
> imin = 0, ntx = 5, irest = 1,
> ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0,
> ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
> nstlim = 50001, dt =0.002,
> tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 12.0,
> jar=1,
> /
> &wt type='DUMPFREQ', istep1=1, /
> &wt type='END', /
> DISANG=dist.RST
> DUMPAVE=dist_vs_t
> LISTIN=POUT
> LISTOUT=POUT
>
>
> And my dist.RST file is:
>
> # Change distance between atoms 1496 and 3647 from 32 A to 5.0 A
> &rst iat=1496,3647, r2=32., rk2 = 50., r2a=5.0, /
>
> # Change angle between atoms 1496, 3647 and 4199 from 0 to 360 degree
> &rst iat=1496,3647,4199, r2=0., rk2 = 50., r2a=360.0, /
>
>
> However from the output, it seems that only the first distance
> restraint is being applied. How can I solve this?
>
> Thanks in advance
> Suchetana Gupta
> IIT Madras
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Received on Fri Apr 07 2017 - 23:30:02 PDT
