Hi, Yao
It seems the GROUP problem not the smd problem, could you send me your
input files(inpcrd, prmtop, mdin. cv.in)
so I can run a test.
Feng
On Tue, Jul 25, 2017 at 3:47 PM, Yao Xiao <yao.xiao26.uga.edu> wrote:
> Hi Feng:
>
>
> I'm trying to follow your instruction and run a short SMD without harmonic
> restraint. Right now my md.in and cv.in looks like:
>
>
> md.in:
>
>
> Restrain all backbone CA atoms
> 10.0
> ATOM 5 5
> ...... ...... ......
> ...... ...... ......
> ATOM 4367 4367
> END
> END
> /
> &smd
> output_file = 'xx_smd.txt'
> output_freq = 10000
> cv_file= 'cv.in'
> /
>
> Everything else in md.in remains unchanged.
>
> cv.in:
>
> cv_file
> &colvar
> cv_type = 'MULTI_RMSD'
> cv_ni = 14, cv_nr = 36
> cv_i = (4618, 4636, 4632, 4628, 4621, 4620, 0, 4646, 4664, 4660, 4656,
> 4649, 4648, 0)
> cv_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)
>
> npath = 2, path = 1, 0, path_mode = 'LINES',
> nharm = 1, harm = 0.0
> /
>
>
> My goal is to steer the MULTI_RMSD value to zero(whatever the starting
> value is). The value 1 in "path" is just arbitrary, because "path" needs to
> contain at least two real numbers. Now I get the following error:
>
> 5. REFERENCE ATOM COORDINATES
>
> default_name
> ----- READING GROUP 1; TITLE:
>
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 0.00000
>
> rfree: End of file on unit 5
>
>
> Since the message says the group has Harm of 0.0, I know its the SMD cv_r
> group rather than the previous cartesian restraint group.
> Could you offer more instructions?
>
> Many thanks
> Yao
>
>
>
>
> ________________________________
> 发件人: Feng Pan <fpan3.ncsu.edu>
> 发送时间: 2017年7月24日 22:27:45
> 收件人: AMBER Mailing List
> 主题: Re: [AMBER] 答复: ncsu_smd codes with pmemd in Amber 16
>
> Hi, Yao
>
> Yes, in the new format the "path" cannot contain a 'X' component according
> to coding reasons. If you want to put the initial value into it, a
> trick is that you can run a very short SMD with harm_strength equal zero,
> check the monitor file and you can get the initial value.
>
> For the GROUP, should be this part
> Restrain all backbone CA atoms
> 10.0
> ATOM 5 5
> ...... ...... ......
> ...... ...... ......
> ATOM 4367 4367
> END
> END
>
> As I know, you should put the END END just behind your group definitions.
>
> Best
> Feng
>
> On Mon, Jul 24, 2017 at 5:55 PM, Yao Xiao <yao.xiao26.uga.edu> wrote:
>
> > Hi, Feng:
> >
> >
> > Thank you very much for your help.
> >
> >
> > Yes, I notice the new input format in amber manual 17, but I still have
> > the some questions:
> >
> >
> > In the old ncsu_smd format, "path" can contain X, which means the intital
> > value of the reaction coordinate. How can I express this concept of
> > initial value in the new input format? According to the manual, "path"
> must
> > contain real numbers. Obviously I don't know the initial value
> beforehand.
> >
> >
> > Also, could you please elaborate on the "GROUP definition? Does that mean
> > the content between "&something" and "/"? In other words, does the former
> > initializes, while the latter ends a group definition? I'm a beginner
> user
> > of Amber so I need some more instructions.
> >
> >
> > Thanks.
> >
> >
> > Best,
> >
> > Yao
> >
> > ________________________________
> > 发件人: Feng Pan <fpan3.ncsu.edu>
> > 发送时间: 2017年7月24日 17:11:33
> > 收件人: AMBER Mailing List
> > 主题: Re: [AMBER] ncsu_smd codes with pmemd in Amber 16
> >
> > Hi, Yao
> >
> > The SMD in pmemd uses a new &smd input format, so you need to change the
> > input styles. Check
> > the new Amber 2017 manual for details.
> >
> > Also, I think you cannot put the SMD block inside the group block. You
> > should finish the GROUP definition
> > first and then write &smd block.
> >
> > Best
> > Feng
> >
> > On Mon, Jul 24, 2017 at 4:58 PM, Yao Xiao <yao.xiao26.uga.edu> wrote:
> >
> > > Dear Amber Developers:
> > >
> > >
> > > I'm trying to use the ncsu_smd codes for steered MD. Basically I want
> to
> > > steer two Glcnac rings to their positions in a known crystal structure.
> > > Below is my MD input file:
> > >
> > >
> > > 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,
> > > /
> > > Restrain all backbone CA atoms
> > > 10.0
> > > ATOM 5 5
> > > ...... ...... ......
> > > ...... ...... ......
> > > ATOM 4367 4367
> > >
> > > /
> > > ncsu_smd
> > > output_file = 'xx_smd.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)
> > >
> > > path = (X,0) path_mode = LINES
> > >
> > > harm = (10.0)
> > >
> > > end variable
> > > end ncsu_smd
> > >
> > > END
> > > END
> > >
> > >
> > > The atom id of the Glcnac rings are defined in "i=" session, and the
> > > target coordinates are defined in "r=" session. By submitting a pmemd
> job
> > > with this input file I got the following error:
> > >
> > >
> > > 5. REFERENCE ATOM COORDINATES
> > >
> > > default_name
> > > ----- READING GROUP 1; TITLE:
> > > ncsu_smd
> > >
> > > rfree: Error decoding variable 1 3 from:
> > > output_file
> > >
> > > I know update 9 has to be applied for compatibility between ncsu_smd
> > codes
> > > and pmemd, and I believe I've done that. Then, my MD input file must be
> > > wrong. My rationale for this MD input file come from Amber manual 16,
> > page
> > > 434, figure 22.7.
> > >
> > > Could somebody help me figure out the issues? Thanks in advance.
> > >
> > > Best,
> > >
> > > Yao Xiao
> > > Research Assistant
> > > Complex Carbohydrate Research Center
> > > The University of Georgia
> > > Athens, GA USA
> > > yx55537.uga.edu
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Feng Pan
> > Ph.D. Candidate
> > North Carolina State University
> > Department of Physics
> > Email: fpan3.ncsu.edu
> > _______________________________________________
> > 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
> >
>
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
> 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
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Wed Jul 26 2017 - 11:00:02 PDT
