Re: [gmx-users] About using GLYCAM force field in Gromacs

[WT Ren]

you can try charmm-gui

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn *

On Tue, May 23, 2017 at 11:20 AM, 维维  wrote:

> Dear Gromacs Users,
>
>   I want to know that if there is a easy way of using GLYCAM force field
> in Gromacs. Thanks in advance!
>
> Best regards
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Re: [gmx-users] Fraction of native contacts.

[WT Ren]

Hi, Prakash：

you can try mdtraj.

http://mdtraj.org/1.8.0/examples/native-contact.html

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn *

On Fri, Apr 28, 2017 at 6:19 PM, B Prakash <4grom...@gmail.com> wrote:

> Dear all,
> I need to calculate fraction of native contacts as a measure of protein
> denaturation. Please suggest ways to do so in Gromacs. I tried to use
> mdmat. Is there a better tool?
>
> Regards,
> Prakash.
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Re: [gmx-users] Distance restraint between two chains' com

[WT Ren]

Dear Justin:

Thanks for your reply

What a pity!

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn*

On Sat, Feb 7, 2015 at 5:34 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 2/6/15 8:47 AM, WT Ren wrote:

 Dear Justin:

 Sorry to bother you again

 When I did a long flat-bottom distance restraint(about 2nm),
 I got the error message: “There is no domain decomposition for 8
 nodes”

 So is there any way to do a long distance restraint properly.


 Restraints limit DD cell size, so you're limited to fewer DD cells or not
 using DD at all (OpenMP only).


 -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] Distance restraint between two chains' com

[WT Ren]

Dear Justin:

Sorry to bother you again

When I did a long flat-bottom distance restraint(about 2nm),
I got the error message: “There is no domain decomposition for 8 nodes”

So is there any way to do a long distance restraint properly.

 Best regards

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn*

On Thu, Feb 5, 2015 at 7:51 PM, WT Ren rener...@gmail.com wrote:

 Dear Justin:

 Many thanks for your reply.
 I would like to test the new feature, but I have no much spare time
 recently.
 So it seems that I have to choose some atoms from the two chains
 seperately,
 and do distance restraint on these atoms.

 Weitong* Ren, PhD student*
 Laboratory of Biophysics
 Department of Physics
 *Nanjing University*
 Nanjing, Jiangsu, PR China
 210093
 tel : +86 025 8359 7226
 *wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn*

 On Thu, Feb 5, 2015 at 7:10 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 2/5/15 2:39 AM, WT Ren wrote:

 Dear Gromacs Users,

 I am trying to apply a distance restraint between two chains' center of
 mass to  prevent them diffusing far away from each other. As I known, the
 pull code seems only can restrain the distance to a reference distance
 with
   harmonic potential, while the distance restraint seems can not be
 applied
 to center of mass.

 So can anyone help on this issue?


 I am assuming that you want to apply some sort of flat-bottom potential,
 to be applied only when the chains move a certain distance.  Indeed the
 pull code cannot do that at present, but a flat-bottom potential is in
 development if you want to test it:

 https://gerrit.gromacs.org/#/c/3947/

 -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] Distance restraint between two chains' com

[WT Ren]

Dear Justin:

Many thanks for your reply.
I would like to test the new feature, but I have no much spare time
recently.
So it seems that I have to choose some atoms from the two chains
seperately,
and do distance restraint on these atoms.

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn*

On Thu, Feb 5, 2015 at 7:10 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 2/5/15 2:39 AM, WT Ren wrote:

 Dear Gromacs Users,

 I am trying to apply a distance restraint between two chains' center of
 mass to  prevent them diffusing far away from each other. As I known, the
 pull code seems only can restrain the distance to a reference distance
 with
   harmonic potential, while the distance restraint seems can not be
 applied
 to center of mass.

 So can anyone help on this issue?


 I am assuming that you want to apply some sort of flat-bottom potential,
 to be applied only when the chains move a certain distance.  Indeed the
 pull code cannot do that at present, but a flat-bottom potential is in
 development if you want to test it:

 https://gerrit.gromacs.org/#/c/3947/

 -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!

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[gmx-users] Distance restraint between two chains' com

[WT Ren]

Dear Gromacs Users,

I am trying to apply a distance restraint between two chains' center of
mass to  prevent them diffusing far away from each other. As I known, the
pull code seems only can restrain the distance to a reference distance with
 harmonic potential, while the distance restraint seems can not be applied
to center of mass.

So can anyone help on this issue?

Best regards

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn*
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[gmx-users] Distance restraint between two chains' com

[WT Ren]

Dear Gromacs Users,

I am trying to apply a distance restraint between two chains' center of
mass to  prevent them diffusing far away from each other. As I known, the
pull code seems only can restrain the distance to a reference distance with
 harmonic potential, while the distance restraint seems can not be applied
to center of mass.

So can anyone help on this issue?

Best regards

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn*
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[gmx-users] Reference group in COM pulling

[WT Ren]

Dear all:
  Recently,  I'm using COM pulling to unfold a protein. So I'm
wondering how the gromacs deal with the reference group. Is the reference
group fixed, constrained or free?
  Many thanks in advance.

Weitong* Ren, PhD student*
Laboratory of Biophysics
Department of Physics
*Nanjing University*
Nanjing, Jiangsu, PR China
210093
tel : +86 025 8359 7226
*wt...@biophy.nju.edu.cn wt...@biophy.nju.edu.cn*
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