[gmx-users] Rupture force definition
Rakesh Mishra
rockinbhu at gmail.com
Thu Feb 1 13:59:56 CET 2018
Dear Justin
Here I am applying pull for two groups with respect to two reference group
as following.
; Pull code
pull = yes
pull_ngroups = 4
pull_ncoords = 1
pull_group1_name = chain_A8 (reference also immobile )
pull_group2_name = chain_B35 (pulling group)
pull_group3_name = chain_A17 (reference also immobile)
pull_group4_name = chain_B26 (pulling)
pull_coord1_type = umbrella ; harmonic biasing force
pull_coord1_geometry = distance ; simple distance increase
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per 1 ns
pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
pull_coord1_start = yes ; define initial COM distance > 0
In above protocol I want to make two reference group as
1-chain_A8 2- chain_A17
and two pull group.
1- chain_B35 2- chain_B26
Bute here "pull_group2_name= chain_B35" is pulling the respective molecule
while "pull_group4_name = chain_B26"
I have used different protocol also as following but it also not working .
as we are not getting pull.f and pull.x file
(as according to you to mention all parameters separately for all groups)
; Pull code
pull_type = umbrella
pull_geometry = distance ;
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 3
pull_ncoords = 1
pull_group0 = chain_A8 ; center of carbon's of bilayer
pull_group1 = chain_B35 ; phosphate atom of 16th PEPC in top
pull_rate1 = 0.04 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
pull_group2 = chain_B26 ; phosphate atom of 56th PEPC in bottom
pull_rate2 = 0.04 ; 0.01 nm per ps = 10 nm per ns
pull_k2 = 1000 ; kJ mol^-1 nm^-2
best
On Mon, Jan 29, 2018 at 10:07 AM, Rakesh Mishra <rockinbhu at gmail.com> wrote:
> Thank you Justin.
>
> I got it and did it also.
>
> On Thu, Jan 25, 2018 at 7:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
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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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
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>
>
>
> --
> * Rakesh Kumar Mishra*
> * (RA)CSD SINP Kolkata, India*
>
> *E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
>
> *Phone n. +91 9473662491 <094736%2062491>, +91877749632*
>
--
* Rakesh Kumar Mishra*
* (RA)CSD SINP Kolkata, India*
*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *
*Phone n. +91 9473662491, +91877749632*
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