[gmx-users] Rupture force definition
jalemkul at vt.edu
Thu Jan 25 14:35:13 CET 2018
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.
> 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
>>> 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
>>> 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 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
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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