[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
>>>>
>>>> ==================================================
>>>>
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>>>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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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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