subject:"\[gmx\-users\] I have questions for tabulated bonded potentials"

Re: [gmx-users] I have questions for tabulated bonded potentials

2016-08-30 Thread Chang Woon Jang

Dear Justin Lemkul,

  I got it. Thank you very much for your help.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:40 PM, Chang Woon Jang 
wrote:

> Dear Justin,
>
>
>Do you mean "Order of parameters"? If I would like to specify for
> table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for
> table_b2.xvg, I need to set 2 after 8.
>
> Am I right?
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang 
> wrote:
>
>> Dear Justin Lemkul,
>>
>> I have seen the 4.2.12 and Table 5.5. However, it does not show the
>> specific example for several tabulated potentials in topol.top file. I
>> created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
>> table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
>> different n values for each interactions.
>>
>> However, 4.2.12 just says that "Multiple tables can be supplied simply by
>> using different values of n, and are applied to the appropriate bonds, as
>> specified in the topology (Table 5.5)".
>>
>> In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
>> no explanation for distingushing several tables to specify different bonded
>> interactions.
>>
>> Thank you.
>>
>> Best regards,
>> Changwoon Jang
>>
>> On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>>>
 Dear Gromacs Users,

   From the above question, I think that I need to specify the each
 bonded interaction in topol.top file. Am I right?

For example,


 [ bond ]
 1  1  2  table_b1.xvg
 2  2  3  table_b2.xvg
 3  3  4  table_b3.xvg


 Is this right format if I have several tabulated potential files in
 topol.top?


>>> No.  Consult Table 5.5 - the function type is 8 (or 9, depending on
>>> whether you need to generate exclusions) and the table number is supplied
>>> as one of the parameters.  See also section 4.2.14.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
>>
>>
>> --
>> Best regards,
>> Changwoon Jang,
>>
>> Postdoctoral Research Fellow
>> Department of Chemical & Biological Engineering, Drexel University
>> 3141 Chestnut Street, Philadelphia, PA 19104
>>
>> Voice: (662) 617-2267
>> E-mail: cj...@drexel.edu
>>
>
>
>
> --
>
>
-- 
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Re: [gmx-users] I have questions for tabulated bonded potentials

2016-08-30 Thread Chang Woon Jang

Dear Justin,


   Do you mean "Order of parameters"? If I would like to specify for
table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for
table_b2.xvg, I need to set 2 after 8.

Am I right?

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang 
wrote:

> Dear Justin Lemkul,
>
> I have seen the 4.2.12 and Table 5.5. However, it does not show the
> specific example for several tabulated potentials in topol.top file. I
> created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
> table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
> different n values for each interactions.
>
> However, 4.2.12 just says that "Multiple tables can be supplied simply by
> using different values of n, and are applied to the appropriate bonds, as
> specified in the topology (Table 5.5)".
>
> In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
> no explanation for distingushing several tables to specify different bonded
> interactions.
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>>
>>> Dear Gromacs Users,
>>>
>>>   From the above question, I think that I need to specify the each
>>> bonded interaction in topol.top file. Am I right?
>>>
>>>For example,
>>>
>>>
>>> [ bond ]
>>> 1  1  2  table_b1.xvg
>>> 2  2  3  table_b2.xvg
>>> 3  3  4  table_b3.xvg
>>>
>>>
>>> Is this right format if I have several tabulated potential files in
>>> topol.top?
>>>
>>>
>> No.  Consult Table 5.5 - the function type is 8 (or 9, depending on
>> whether you need to generate exclusions) and the table number is supplied
>> as one of the parameters.  See also section 4.2.14.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> Best regards,
> Changwoon Jang,
>
> Postdoctoral Research Fellow
> Department of Chemical & Biological Engineering, Drexel University
> 3141 Chestnut Street, Philadelphia, PA 19104
>
> Voice: (662) 617-2267
> E-mail: cj...@drexel.edu
>



-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj...@drexel.edu
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] I have questions for tabulated bonded potentials

2016-08-30 Thread Justin Lemkul




On 8/30/16 8:35 PM, Chang Woon Jang wrote:

Dear Justin Lemkul,

I have seen the 4.2.12 and Table 5.5. However, it does not show the
specific example for several tabulated potentials in topol.top file. I
created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
different n values for each interactions.

However, 4.2.12 just says that "Multiple tables can be supplied simply by
using different values of n, and are applied to the appropriate bonds, as
specified in the topology (Table 5.5)".

In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
no explanation for distingushing several tables to specify different bonded
interactions.



In section 4.2.14:

"For each interaction, the force constant k and the table number n are specified 
in the topology."


In Table 5.5 (in the column "Order of parameters and their units"):

table number (≥ 0); k (kJ mol−1)

So for table_b1.xvg with k = 1000 (just an example) to be applied to atoms 1 
and 2:

[ bonds ]
; ai aj func table k
  1   2   8   11000

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
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Re: [gmx-users] I have questions for tabulated bonded potentials

2016-08-30 Thread Chang Woon Jang

Dear Justin Lemkul,

I have seen the 4.2.12 and Table 5.5. However, it does not show the
specific example for several tabulated potentials in topol.top file. I
created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg,
table_a2.xvg ... table_a6.xvg, table_d1.xvg  table_d4.xvg. Those are
different n values for each interactions.

However, 4.2.12 just says that "Multiple tables can be supplied simply by
using different values of n, and are applied to the appropriate bonds, as
specified in the topology (Table 5.5)".

In Table 5.5, tabulated bond funct is specified with 8 or 9, but there is
no explanation for distingushing several tables to specify different bonded
interactions.

Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 8:19 PM, Justin Lemkul  wrote:

>
>
> On 8/30/16 8:11 PM, Chang Woon Jang wrote:
>
>> Dear Gromacs Users,
>>
>>   From the above question, I think that I need to specify the each
>> bonded interaction in topol.top file. Am I right?
>>
>>For example,
>>
>>
>> [ bond ]
>> 1  1  2  table_b1.xvg
>> 2  2  3  table_b2.xvg
>> 3  3  4  table_b3.xvg
>>
>>
>> Is this right format if I have several tabulated potential files in
>> topol.top?
>>
>>
> No.  Consult Table 5.5 - the function type is 8 (or 9, depending on
> whether you need to generate exclusions) and the table number is supplied
> as one of the parameters.  See also section 4.2.14.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>

-- 
Best regards,
Changwoon Jang,

Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104

Voice: (662) 617-2267
E-mail: cj...@drexel.edu
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] I have questions for tabulated bonded potentials

2016-08-30 Thread Justin Lemkul




On 8/30/16 8:11 PM, Chang Woon Jang wrote:

Dear Gromacs Users,

  From the above question, I think that I need to specify the each
bonded interaction in topol.top file. Am I right?

   For example,


[ bond ]
1  1  2  table_b1.xvg
2  2  3  table_b2.xvg
3  3  4  table_b3.xvg


Is this right format if I have several tabulated potential files in
topol.top?



No.  Consult Table 5.5 - the function type is 8 (or 9, depending on whether you 
need to generate exclusions) and the table number is supplied as one of the 
parameters.  See also section 4.2.14.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] I have questions for tabulated bonded potentials

2016-08-30 Thread Chang Woon Jang

Dear Gromacs Users,

  From the above question, I think that I need to specify the each
bonded interaction in topol.top file. Am I right?

   For example,

[ bond ]
1  1  2  table_b1.xvg
2  2  3  table_b2.xvg
3  3  4  table_b3.xvg

Is this right format if I have several tabulated potential files in
topol.top?

Thank you.

Best regards,
Changwoon Jang

On Tue, Aug 30, 2016 at 4:31 PM, Chang Woon Jang 
wrote:

> Dear Gromacs Users,
>
> I have several bond, angle, dihedral potentials named table_b1.xvg,
> table_b2.xvg, table_b3.xvg ...table_a1.xvg, table_a2.xvg ... table_d1.xvg,
> table_d2.xvg, table_d3.xvg, table_d4.xvg.
>
> In my system, there are 6 types of beads (A, B, C, D, E, F). How can I
> assign each potential table to specific interactions. For example,
> table_b1.xvg is A-B bond interaction, table_a1.xvg is A-B-A angle
> interactions end so on.
>
> Thank you.
>
>
> Best regards,
> Changwoon Jang,
>
>
-- 
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[gmx-users] I have questions for tabulated bonded potentials

2016-08-30 Thread Chang Woon Jang

Dear Gromacs Users,

I have several bond, angle, dihedral potentials named table_b1.xvg,
table_b2.xvg, table_b3.xvg ...table_a1.xvg, table_a2.xvg ... table_d1.xvg,
table_d2.xvg, table_d3.xvg, table_d4.xvg.

In my system, there are 6 types of beads (A, B, C, D, E, F). How can I
assign each potential table to specific interactions. For example,
table_b1.xvg is A-B bond interaction, table_a1.xvg is A-B-A angle
interactions end so on.

Thank you.


Best regards,
Changwoon Jang,
-- 
Gromacs Users mailing list

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Re: [gmx-users] I have questions for tabulated bonded potentials

Re: [gmx-users] I have questions for tabulated bonded potentials

Re: [gmx-users] I have questions for tabulated bonded potentials

Re: [gmx-users] I have questions for tabulated bonded potentials

Re: [gmx-users] I have questions for tabulated bonded potentials

Re: [gmx-users] I have questions for tabulated bonded potentials

[gmx-users] I have questions for tabulated bonded potentials

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