Hi Dr. Roitberg,
It is fine when I selected only two atoms. But I need to pull many atoms
together.
Thank you!
Sincerely,
Pinky
On Thu, Feb 25, 2021 at 2:22 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
> Hi
>
> Try first with just a couple of atoms in your ref.RST file like:
>
> &rst
> iat=2709,1365,
> r2=72.67,
> r2a=0.0,
> rk2=7.2,
> &end
>
> to see if it works.
>
> Second, are you sure you want to have r2a = 0.0 ? that will try to have
> the two gropus of atoms get to ZERO distance, which I believe will (and
> should) break everything).
>
> Adrian
>
>
> On 2/25/21 3:14 PM, Pinky Mazumder wrote:
> > [External Email]
> >
> > Hi,
> >
> > I am trying to pull one layer (group of atoms) towards another group of
> > atoms using the steered molecular dynamics. I have taken the center of
> mass
> > of both groups. The (.RST) and (pull.in) file is given below:
> >
> > &rst
> > iat=-1,-1,
> > r2=72.67,
> > r2a=0.0,
> > rk2=7.2,
> >
> >
> igr1=2709,2730,2751,2772,2793,2814,2835,2856,2877,2898,2919,2940,2961,2982,3003,3024,3048,3069,3090,3111,3132,3153,3174,3195,3216,3237,3258,3279,3300,3321,3342,3363,3386,3407,3428,3449,3470,3491,3512,3533,3554,3575,3596,3617,3638,3659,3680,3701,3725,3746,3767,3788,3809,3830,3851,3872,3893,3914,3935,3956,3977,3998,4019,4040,
> >
> >
> igr2=1365,1386,1407,1428,1449,1470,1491,1512,1533,1554,1575,1596,1617,1638,1659,1680,1704,1725,1746,1767,1788,1809,1830,1851,1872,1893,1914,1935,1956,1977,1998,2019,2042,2063,2084,2105,2126,2147,2168,2189,2210,2231,2252,2273,2294,2315,2336,2357,2381,2402,2423,2444,2465,2486,2507,2528,2549,2570,2591,2612,2633,2654,2675,2696,
> >
> > &end
> >
> > ASMD Simulation Example MD Input
> > &cntrl
> > imin = 0, nstlim = 20000, dt = 0.002,
> > ntx = 1, temp0 = 300.0,
> > ntt = 3, gamma_ln=5.0
> > ntc = 2, ntf = 2, ntb =1,
> > ntwx = 1000, ntwr = 1000, ntpr = 1000,
> > cut = 10.0, ig=-1, ioutfm=1,
> > irest = 0, jar=1,
> > /
> > &wt type='DUMPFREQ', istep1=1, /
> > &wt type='END', /
> > DISANG=ref.RST
> > DUMPAVE=ref_vs_t
> > LISTIN=POUT
> > LISTOUT=POUT
> >
> > When I am running simulation, it gives following error:
> > Restraints will be read from file: ref.RST
> > Here are comments from the DISANG input file:
> >
> >
> > *jar option running In Jarzynsky runs, there must only one restrain,
> > stopping program*
> >
> > Any help would be appreciated.
> >
> > Thank you.
> >
> > Sincerely,
> > Pinky
> > --
> > Pinky Mazumder
> > PhD Student
> > University of Alabama
> > USA
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=CqzFAWPdYovbmAUpZxFIQmJyYQsg1VPbDKFo44ZS3Mk&s=E1NdBtoYo7MxU2SXucvPmNBQvS1_Fm682XT-ZCq6FrQ&e=
>
> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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>
--
Pinky Mazumder
PhD Student
University of Alabama
USA
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Received on Fri Feb 26 2021 - 08:00:02 PST
