[gmx-users] Rupture force definition

[Justin Lemkul]

On 1/25/18 2:41 AM, Rakesh Mishra wrote:
> Thanks for reply.
>
> Dear Justin
>
> Is it possible to transform .xtc file in the form of .pdb formate
> excluding solvent and ion molecules simultaneously.
> I am familiar to do this with "trjconv" command. But by using this we can
> transform .xtc file in the form of .pdb formate,
> where water molecules and ions gets also present in the .pdb formate. How
> it is possible to save only system coordinates
> rather than solvent ( water molecules ) molecules and ions  at the same
> time .

trjconv (like most GROMACS tools) lets you pick whatever subset of atoms 
you want. Choose an appropriate group for output that suits your needs.

-Justin

>
>
>
>
> On Wed, Jan 24, 2018 at 6:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/24/18 5:02 AM, Rakesh Mishra wrote:
>>
>>> Dear Justin
>>>
>>> Thank you very much  for removing the doubts .
>>> Let me extend  my query in this respect again. As according to pull code
>>> formate which is  discussed in your testing work of umbrella sampling .
>>> Please have a rough look.
>>>
>>> Pull code
>>> pull                    = yes
>>> pull_ngroups            = 2
>>> pull_ncoords            = 1
>>> pull_group1_name        = chain_B
>>> pull_group2_name        = chain_A
>>> pull_coord1_type        = umbrella      ; harmonic biasing force
>>> pull_coord1_geometry    = distance      ; simple distance increase
>>> pull_coord1_groups      =  1 2
>>> pull_coord1_dim         = Y N N
>>> pull_coord1_rate        = 0.0005          ; 0.0005 nm per ps = 5 nm per 10
>>> ns
>>> pull_coord1_k           = 400          ; kJ mol^-1 nm^-2
>>> pull_coord1_start       = yes           ; define initial COM distance > 0
>>>
>>> As according to some explanation on the net,  I found  that  in the Pull
>>> code written above,
>>>
>>> "pull_group1_name = chain_B "   gromacs read it as a reference group by
>>> default &
>>> "pull_group2_name = chain_A"    gromacs read it as a pull group by
>>> default.
>>>
>>> But suppose, we want to pull 2 or more groups eg.  B2 & B3 in the same
>>> system and which are having
>>> two respective reference group A2 & A3 w. r. t. pulled groups  B2 & B3.
>>> Then how to define these one in above code.
>>>
>>> I mean If I have  A1, A2, and A3 three pull group ( which we want to pull)
>>> and corresponding to these we have three
>>> reference group B1 , B2 and B3. We are pulling all in the same direction
>>> (+x  direction ).
>>> then how to define these simultaneously in above pull code.
>>>
>>> will I need to define rate for all these pull group separately ( three
>>> times) or if rate value is same then no need to
>>>    define three times corresponding to these three pull groups.
>>>
>> You can define any number of groups to be used in any number of biasing
>> potentials. Each needs its own complete definition (geometry, dimensions,
>> rate, force constant, etc). Get rid of the notion of "reference" and "pull
>> group" in this application; groups define the two ends of a reaction
>> coordinate, nothing more.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================