Hi Yao
You can use smd in pmemd and in gpu with Amber 16 and a patch, using the
ncsu codes. Please look at the amber16 manual for that, sinc ethe input
format has changed.
adrian
On 7/10/17 5:32 PM, Yao Xiao wrote:
> Dear Amber Developers:
>
>
> I'm currently trying to run some steered MDs with pmemd. I know many of the sMD features are for sander only, but my systems are too big(~350 protein residues and at least 200ns simulation time) for sander. If I use sander they will take too long to finish. I only know two ways to turn on sMD: ncsu_smd or jar=1. Below is my sample MD input file, which should work for sander:
>
>
> MD production run at NPT
> # control section
> &cntrl
> irest = 1,
> ntx = 5, ntb = 2, ntp = 1,ntwprt=4675
> cut = 8.0, ntt = 3, gamma_ln = 2,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0, tautp = 2.0,
> nstlim = 100000000, dt = 0.002,
> ntpr = 30000, ntwx = 10000, ntwv = 0, ntwe = 0,
> nmropt = 0, ntr=1, ioutfm =1,iwrap=1,ig = -1,
> /
>
> ncsu_smd
> output_file= 'FILE.txt'
> output_freq= 10000
> variable
> type=MULTI_RMSD
> i=(4618, 4636, 4632, 4628, 4621, 4620, 0, 4646, 4664, 4660, 4656, 4649, 4648, 0)
> r=(47.228, 38.993, 29.383,
> 48.172, 39.346, 30.539,
> 47.472, 40.312, 31,486,
> 47.010, 41.547, 30.733,
> 46.155, 41.145, 29.525,
> 46.917, 40.161, 28.700,
>
> 46.955, 30.894, 40.394,
> 47.928, 31.919, 41.011,
> 49.322, 31.437, 40.654,
> 49.559, 30.004, 41.103,
> 48.484, 29.062, 40.595,
> 47.239, 29.616, 40.816)
>
> harm = (10.0)
> path = (X,0) path_mode = LINES
> end variable
> end ncsu_smd
>
>
> In the above MD input file, I'm trying to steer two Glcnac rings (defined as two groups of atoms in "i=" section), towards their position in a known crystal structure(defined as two groups of coordinates in "r=" section.) ,applying a harmonic restraint constant of 10.0.
>
> This should work for sander, but I just have to use pmend for speed. Since the ncsu_smd codes works for sander only, it appears that I can only do it through jar=1, which requires a restraint file specified by DISANG. It looks to me that whatever the available NMR restraint variable type is, it has to be defined using real atoms present in the system. However, the variable I'm trying to define here involves a group of real atoms and a group of coordinates(no atom is present at these coordinates).
>
> So to put it together: what NMR restraint variable type can be defined using a group of atoms and a group of coordinates, and also works for pmemd?
>
> Thank you for providing instructions in advance.
>
>
>
> Yao Xiao
> Research Assistant
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA, USA
> yx55537.uga.edu
>
>
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Jul 10 2017 - 15:00:03 PDT
