not really... You need to pull the CENTER of mass of lots of atoms,
which is not the same, right ?
I believe the error you got in your second attempt was related to the
maximum number of atoms you can have in a given group.
Look at page 27 of the AMBER 20 manual.
You can have MAXIMUM 200 atoms in a group, and it is possible you have more.
So, there are two options:
1. Change the value of I think the variable MAXGRP in the actual code,
and recompile. If you never changed the code/recompiled, I would not
recommend this.
2. Reduce the number of atoms in your group mask. I am betting you can
look at the atoms you choose and reduced it by half. For example, if you
list all CA atoms in your molecule, list instead every OTHER CA atom.
More general comments.
Your input (and I do think you want to use jar, NOT nmropt)
which is WAY too fast
&rst
iat=2709,1365,
r2=72.67,
r2a=0.0,
rk2=7.2,
&end
Your input (and I do think you want to use jar, NOT nmropt)
is trying to go from 72 A to zero A in 20K steps, which is WAY to fast.
Moreover, you truly do not wan to go to zero ! You want to go to the
minimal distance possible between your two groups of atoms.
Adrian
On 2/26/21 10:43 AM, Pinky Mazumder wrote:
> [External Email]
>
> 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
>>
>>
>> _______________________________________________
>> 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=g2rPo9g3dRq2TKBjbS-t7nLEDfeLo3QTb0jh7o5gt9w&s=QoaWPYejd0MOBUO4s85XaUR9hrLrqoPUAdG0eb20LKM&e=
>>
>
> --
> 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=g2rPo9g3dRq2TKBjbS-t7nLEDfeLo3QTb0jh7o5gt9w&s=QoaWPYejd0MOBUO4s85XaUR9hrLrqoPUAdG0eb20LKM&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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Received on Fri Feb 26 2021 - 08:30:02 PST
