[gmx-users] simulation with position constraint by a harmonic potential

Liu, Liang liu4gre at gmail.com
Tue Sep 27 00:13:10 CEST 2011


Thanks for the information.

It looks the pdb2gmx can generate the posre.itp file and what I use is "pdb2gmx
-ignh -ff amber03 -f *.pdb -o *.gro -p *.top -water spce".
The file shows:
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained."
[ position_restraints ]
; atom  type      fx      fy      fz
     1     1  1000  1000  1000
     3     1  1000  1000  1000
     6     1  1000  1000  1000
     8     1  1000  1000  1000
     9     1  1000  1000  1000
    11     1  1000  1000  1000
    12     1  1000  1000  1000
    14     1  1000  1000  1000
    15     1  1000  1000  1000
    16     1  1000  1000  1000
    17     1  1000  1000  1000
    20     1  1000  1000  1000
    21     1  1000  1000  1000
    23     1  1000  1000  1000
    24     1  1000  1000  1000
    25     1  1000  1000  1000
    27     1  1000  1000  1000
    29     1  1000  1000  1000
    31     1  1000  1000  1000
    32     1  1000  1000  1000
    33     1  1000  1000  1000
    34     1  1000  1000  1000
    35     1  1000  1000  1000
    36     1  1000  1000  1000
    39     1  1000  1000  1000
    41     1  1000  1000  1000
    42     1  1000  1000  1000
    44     1  1000  1000  1000
    45     1  1000  1000  1000
    47     1  1000  1000  1000
    49     1  1000  1000  1000
    50     1  1000  1000  1000
    51     1  1000  1000  1000
    53     1  1000  1000  1000
    54     1  1000  1000  1000
    55     1  1000  1000  1000
    57     1  1000  1000  1000
    59     1  1000  1000  1000
    61     1  1000  1000  1000
    62     1  1000  1000  1000
    63     1  1000  1000  1000
    64     1  1000  1000  1000
    65     1  1000  1000  1000
    66     1  1000  1000  1000
    69     1  1000  1000  1000
    71     1  1000  1000  1000
    72     1  1000  1000  1000
    74     1  1000  1000  1000
    75     1  1000  1000  1000
    77     1  1000  1000  1000
    78     1  1000  1000  1000
    79     1  1000  1000  1000
    80     1  1000  1000  1000
    81     1  1000  1000  1000
    83     1  1000  1000  1000
    84     1  1000  1000  1000
    87     1  1000  1000  1000
    88     1  1000  1000  1000
    89     1  1000  1000  1000
    91     1  1000  1000  1000
    93     1  1000  1000  1000
    95     1  1000  1000  1000
    96     1  1000  1000  1000
    97     1  1000  1000  1000
    98     1  1000  1000  1000
    99     1  1000  1000  1000
   100     1  1000  1000  1000
   103     1  1000  1000  1000
   105     1  1000  1000  1000
   106     1  1000  1000  1000
   108     1  1000  1000  1000
   109     1  1000  1000  1000
   111     1  1000  1000  1000
   113     1  1000  1000  1000
   114     1  1000  1000  1000
   117     1  1000  1000  1000
   118     1  1000  1000  1000
   119     1  1000  1000  1000
   120     1  1000  1000  1000
   122     1  1000  1000  1000
   124     1  1000  1000  1000
   126     1  1000  1000  1000
   127     1  1000  1000  1000
   128     1  1000  1000  1000
   129     1  1000  1000  1000
   130     1  1000  1000  1000
   131     1  1000  1000  1000
   134     1  1000  1000  1000
   136     1  1000  1000  1000
   137     1  1000  1000  1000
   139     1  1000  1000  1000
   140     1  1000  1000  1000
   142     1  1000  1000  1000
   144     1  1000  1000  1000
   145     1  1000  1000  1000
   146     1  1000  1000  1000
   148     1  1000  1000  1000
   149     1  1000  1000  1000
   150     1  1000  1000  1000
   152     1  1000  1000  1000
   154     1  1000  1000  1000
   156     1  1000  1000  1000
   157     1  1000  1000  1000
   158     1  1000  1000  1000
   159     1  1000  1000  1000
   160     1  1000  1000  1000
   161     1  1000  1000  1000
   164     1  1000  1000  1000
   166     1  1000  1000  1000
   167     1  1000  1000  1000
   169     1  1000  1000  1000
   170     1  1000  1000  1000
   172     1  1000  1000  1000
   174     1  1000  1000  1000
   175     1  1000  1000  1000
   176     1  1000  1000  1000
   178     1  1000  1000  1000
   179     1  1000  1000  1000
   180     1  1000  1000  1000
   182     1  1000  1000  1000
   184     1  1000  1000  1000
   186     1  1000  1000  1000
   187     1  1000  1000  1000
   188     1  1000  1000  1000
   189     1  1000  1000  1000
   190     1  1000  1000  1000
   191     1  1000  1000  1000
   194     1  1000  1000  1000
   196     1  1000  1000  1000
   197     1  1000  1000  1000
   199     1  1000  1000  1000
   200     1  1000  1000  1000
   202     1  1000  1000  1000
   203     1  1000  1000  1000
   204     1  1000  1000  1000
   205     1  1000  1000  1000
   208     1  1000  1000  1000
   209     1  1000  1000  1000
   211     1  1000  1000  1000
   212     1  1000  1000  1000
   213     1  1000  1000  1000
   215     1  1000  1000  1000
   217     1  1000  1000  1000
   219     1  1000  1000  1000
   220     1  1000  1000  1000
   221     1  1000  1000  1000
   222     1  1000  1000  1000
   223     1  1000  1000  1000
   224     1  1000  1000  1000
   227     1  1000  1000  1000
   229     1  1000  1000  1000
   230     1  1000  1000  1000
   232     1  1000  1000  1000
   233     1  1000  1000  1000
   235     1  1000  1000  1000
   236     1  1000  1000  1000
   237     1  1000  1000  1000
   238     1  1000  1000  1000
   241     1  1000  1000  1000
   242     1  1000  1000  1000
   244     1  1000  1000  1000
   245     1  1000  1000  1000
   246     1  1000  1000  1000
   248     1  1000  1000  1000
   250     1  1000  1000  1000
   252     1  1000  1000  1000
   253     1  1000  1000  1000
   254     1  1000  1000  1000
   255     1  1000  1000  1000
   256     1  1000  1000  1000
   257     1  1000  1000  1000
   260     1  1000  1000  1000
   262     1  1000  1000  1000
   263     1  1000  1000  1000
   265     1  1000  1000  1000
   266     1  1000  1000  1000
   268     1  1000  1000  1000
   269     1  1000  1000  1000
   270     1  1000  1000  1000
   271     1  1000  1000  1000
   274     1  1000  1000  1000
   275     1  1000  1000  1000
   277     1  1000  1000  1000
   278     1  1000  1000  1000
   279     1  1000  1000  1000
   281     1  1000  1000  1000
   283     1  1000  1000  1000
   285     1  1000  1000  1000
   286     1  1000  1000  1000
   287     1  1000  1000  1000
   288     1  1000  1000  1000
   289     1  1000  1000  1000
   290     1  1000  1000  1000
   293     1  1000  1000  1000
   295     1  1000  1000  1000
   296     1  1000  1000  1000
   298     1  1000  1000  1000
   299     1  1000  1000  1000
   301     1  1000  1000  1000
   302     1  1000  1000  1000
   303     1  1000  1000  1000
   304     1  1000  1000  1000
   305     1  1000  1000  1000
   307     1  1000  1000  1000
   308     1  1000  1000  1000
   311     1  1000  1000  1000
   312     1  1000  1000  1000
   313     1  1000  1000  1000
   315     1  1000  1000  1000
   317     1  1000  1000  1000
   319     1  1000  1000  1000
   320     1  1000  1000  1000
   321     1  1000  1000  1000
   322     1  1000  1000  1000
   323     1  1000  1000  1000
   324     1  1000  1000  1000
   327     1  1000  1000  1000
   329     1  1000  1000  1000
   330     1  1000  1000  1000
   332     1  1000  1000  1000
   333     1  1000  1000  1000
   335     1  1000  1000  1000
   337     1  1000  1000  1000
   338     1  1000  1000  1000
   341     1  1000  1000  1000
   342     1  1000  1000  1000
   343     1  1000  1000  1000
   344     1  1000  1000  1000
   346     1  1000  1000  1000
   348     1  1000  1000  1000
   350     1  1000  1000  1000
   351     1  1000  1000  1000
   352     1  1000  1000  1000
   353     1  1000  1000  1000
   354     1  1000  1000  1000
   355     1  1000  1000  1000
   358     1  1000  1000  1000
   360     1  1000  1000  1000
   361     1  1000  1000  1000
   363     1  1000  1000  1000
   364     1  1000  1000  1000
   366     1  1000  1000  1000
   367     1  1000  1000  1000
   368     1  1000  1000  1000
   369     1  1000  1000  1000
   372     1  1000  1000  1000
   373     1  1000  1000  1000
   375     1  1000  1000  1000
   376     1  1000  1000  1000
   377     1  1000  1000  1000
   379     1  1000  1000  1000
   381     1  1000  1000  1000
   383     1  1000  1000  1000
   384     1  1000  1000  1000
   385     1  1000  1000  1000
   386     1  1000  1000  1000
   387     1  1000  1000  1000
   388     1  1000  1000  1000
   391     1  1000  1000  1000
   393     1  1000  1000  1000
   394     1  1000  1000  1000
   396     1  1000  1000  1000
   397     1  1000  1000  1000
   399     1  1000  1000  1000
   401     1  1000  1000  1000
   402     1  1000  1000  1000
   403     1  1000  1000  1000
   405     1  1000  1000  1000
   406     1  1000  1000  1000
   407     1  1000  1000  1000
   409     1  1000  1000  1000
   411     1  1000  1000  1000
   413     1  1000  1000  1000

So how to adjust the force constraint to the harmonic poteitial E =
k(r-r0)^2, with different values of k?

I am totally a new user of Gromacs, even MD simulation. Please help, Thanks
a lot.

On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Liu, Liang wrote:
>
>> Firstly I want to thank for your reply, yes, it should be position
>> restraint.
>>
>> I don't know how to reply in the thread, actually that was my first post.
>> Therefore I have to ask you here, hope it also work to you.
>>
>>
> Simply reply to the message.  The discussion needs to stay on the list.
>  The members are not private tutors.
>
>  My question is how to perform a position restraint simulation with the
>> heavy atom constrained to its initial position by a harmonic potential
>> E=k(r-r0)^2,
>> which changes with k equal to 0, 10, 20, ..., 90, 100, and so on?
>>
>>
> You can adjust the force constant in the posre.itp file.  There is no
> automated way of decreasing or increasing a restraint; independent
> simulations must be run on the different topologies.
>
> -Justin
>
>  Thanks, and any helps will be highly appreciated.
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>



-- 
Best,
Liang Liu
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