Re: [gmx-users] User-Specified LJ Epsilon and Sigma

[Maryam Kowsar]

Hi dan
I think that's not possible to change forcefield parameters and use the old
defined forcefield like opls. When you change the parameters in .itp you
should introduce your own forcefield. Try to have all the needed files of
forcefield in a new folder and use that during making topology.

On Tuesday, September 8, 2015, Phwey Gil  wrote:

> Hi,
>
> I am looking to specify my own parameters for LJ parameters. Using the OPLS
> forcefield, I only want to change the LJ parameters of some atoms.
>
> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
> change the LJ parameters for the hydrogens in C8H16O2 only.
>
> I have tried specifying [ atomtypes ] in various places (In .top or .itp)
> using the following format:
>
>  [ atomtypes ]
>   H H  1.008  0.450 A   5.66387665E-4
> 2.80730518E-7
>
> But I was not successful; I checked topol.tpr and the numbers are according
> to OPLS and not my specified values.
>
> Can someone give me advice on how to do this? I've checked the forums and I
> was not successful at finding the correct information.
>
> Best Regards,
>
> Dan
>
> --
> Dan Gil
> Case Western Reserve University | Class of 2016
> Researcher, Department of Chemical Engineering
> ps...@case.edu 
> --
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Re: [gmx-users] User-Specified LJ Epsilon and Sigma

[Justin Lemkul]

On 9/9/15 7:29 AM, Maryam Kowsar wrote:

Hi dan
I think that's not possible to change forcefield parameters and use the old
defined forcefield like opls. When you change the parameters in .itp you
should introduce your own forcefield. Try to have all the needed files of
forcefield in a new folder and use that during making topology.



This is not true. Any force field can be modified or extended. A local copy of a 
modified force field is a safe recommendation, but in the case of simply adding 
new atom types, there's little harm that can be done.


-Justin


On Tuesday, September 8, 2015, Phwey Gil  wrote:


Hi,

I am looking to specify my own parameters for LJ parameters. Using the OPLS
forcefield, I only want to change the LJ parameters of some atoms.

I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
change the LJ parameters for the hydrogens in C8H16O2 only.

I have tried specifying [ atomtypes ] in various places (In .top or .itp)
using the following format:

  [ atomtypes ]
   H H  1.008  0.450 A   5.66387665E-4
2.80730518E-7

But I was not successful; I checked topol.tpr and the numbers are according
to OPLS and not my specified values.

Can someone give me advice on how to do this? I've checked the forums and I
was not successful at finding the correct information.

Best Regards,

Dan

--
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
ps...@case.edu 
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--
==

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] User-Specified LJ Epsilon and Sigma

[Maryam Kowsar]

Hi justin
Actually i modified the forcefield parameters to introduce atoms that are
not present in that. I think you are right in the case that we want to
change bonded or nonbonded parameters in the forcefield

On Wednesday, September 9, 2015, Justin Lemkul  wrote:

>
>
> On 9/9/15 7:29 AM, Maryam Kowsar wrote:
>
>> Hi dan
>> I think that's not possible to change forcefield parameters and use the
>> old
>> defined forcefield like opls. When you change the parameters in .itp you
>> should introduce your own forcefield. Try to have all the needed files of
>> forcefield in a new folder and use that during making topology.
>>
>>
> This is not true. Any force field can be modified or extended. A local
> copy of a modified force field is a safe recommendation, but in the case of
> simply adding new atom types, there's little harm that can be done.
>
> -Justin
>
> On Tuesday, September 8, 2015, Phwey Gil  wrote:
>>
>> Hi,
>>>
>>> I am looking to specify my own parameters for LJ parameters. Using the
>>> OPLS
>>> forcefield, I only want to change the LJ parameters of some atoms.
>>>
>>> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
>>> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
>>> change the LJ parameters for the hydrogens in C8H16O2 only.
>>>
>>> I have tried specifying [ atomtypes ] in various places (In .top or .itp)
>>> using the following format:
>>>
>>>   [ atomtypes ]
>>>H H  1.008  0.450 A   5.66387665E-4
>>> 2.80730518E-7
>>>
>>> But I was not successful; I checked topol.tpr and the numbers are
>>> according
>>> to OPLS and not my specified values.
>>>
>>> Can someone give me advice on how to do this? I've checked the forums
>>> and I
>>> was not successful at finding the correct information.
>>>
>>> Best Regards,
>>>
>>> Dan
>>>
>>> --
>>> Dan Gil
>>> Case Western Reserve University | Class of 2016
>>> Researcher, Department of Chemical Engineering
>>> ps...@case.edu 
>>> --
>>> 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 .
>>>
>>>
> --
> ==
>
> 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
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[gmx-users] Multiple membrane proteins in complex bilayer (martini)

[Kathrin Hadasch]

Hey you all,
I'm searching for a way to insert and embed multiple(!) copies of the 
same protein in a complex, presimulated membrane patch (all martini-cg). 
I've tryed lambada for insertion, but I couldn't get it to work with 
more than one protein. I've tried to translate the protein to a (4 4 0) 
vector with editconf in the lambada script, but I get following error:
Modification of non-creatable array value attempted, subscript -6 at 
/home/lambada/modules/protein.pm line 281.
For insertion via vmd, I have no clue how to generate a psf file for 
martini-lipids.

Any suggestions how I could make it work?
Best regards and thanks in advance,
Kathrin
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[gmx-users] g_hbond

[Shahid Nayeem]

Dear all
I have used g_hbond with -hbn -hbm flag to get .ndx file and .xpm file.
Then with xpm2ps I converted .xpm to .eps file. I get half the number of
rows in .eps file as compared to .ndx file. when using Justins perl script
I got summary of existence file and here 12 bonds are shown but in .eps
file only 6 rows are plotted. I know that the bonds are plotted in reverse
order but here only half number of bonds are plotted in .eps file. please
help to resolve this issue.

shahid
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Re: [gmx-users] User-Specified LJ Epsilon and Sigma

[Phwey Gil]

Thank you for your help, Justin, Maryam, and Mark.

By following your advice, I was able to use my own LJ parameters for my
molecule. I used the following lines to be able to change atom X.

*In the topology.top:*

; Include forcefield parameters
#include "ffoplsaa.itp"
*#include "molecule.itp"*

*In molecule.itp:*

*[ atomtypes ]*
* ;name bondtype   masscharge   ptype   sigmaepsilon*
*  X   1  18.998   -0.120   A 2.5e-01
 1.25520e-01*

 [ moleculetype ]
PFOA 3

 [ atoms ]
 1   opls_961  1   PFOACX3  1  0.360 12.011
 2   opls_962  1   PFOACX2  2  0.240 12.011
 3   opls_962  1   PFOACX2  3  0.240 12.011
 4   opls_962  1   PFOACX2  4  0.240 12.011
 5   opls_962  1   PFOACX2  5  0.240 12.011
 6   opls_962  1   PFOACX2  6  0.240 12.011
 7   opls_962  1   PFOACX2  7  0.240 12.011
 8   opls_267  1   PFOACoo  8  0.520 12.011
 *9   X 1   PFOA  X  1*
*10   X 1   PFOA  X  1*
*11   X 1   PFOA  X  2*
*12   X 1   PFOA  X  2*
*13   X 1   PFOA  X  3*
*14   X 1   PFOA  X  3*
*15   X 1   PFOA  X  4*
*16   X 1   PFOA  X  4*
... *and so on...*

Sincerely,

Dan

On Wed, Sep 9, 2015 at 2:50 PM, Mark Abraham 
wrote:

> Hi,
>
> On Wed, Sep 9, 2015 at 7:55 PM Phwey Gil  wrote:
>
> > Hi Justin, Maryam,
> >
> > My initial problem was that I did not specify the atom types as Justin
> > said. Now I am able to change the masses and charges easily, but there
> are
> > still some problems with implementing the lennard-jones potential.
> >
> > In my .itp file I write:
> >  [ atomtypes ]
> >  X  1  7.777  0.450  A  2  3
> >
> > Where X is the atom in question, and I have made up numbers to see how
> they
> > appear in topol.tpr. I was able to see that the masses and charges can be
> > implemented straightforwardly. However, the C6 and C12 parameters are not
> > (2 and 3). The output values found in topol.tpr are:
> >
> >  functype[9]=LJ_SR, c6= 1.41771114e+00, c12= 3.59777004e-01
> >
>
> LJ parameters for the two atom types involved in an interaction combine
> according to the equations in chapter 4 of the manual. There's been some
> pre-computation already.
>
> Additionally, [ Bonds ] do not appear in the topol.tpr either.
> >
>
> Well, don't ask grompp to convert your bonds into constraints ;-)
>
> Mark
>
>
> > On Wed, Sep 9, 2015 at 7:43 AM, Maryam Kowsar 
> > wrote:
> >
> > > Hi justin
> > > Actually i modified the forcefield parameters to introduce atoms that
> are
> > > not present in that. I think you are right in the case that we want to
> > > change bonded or nonbonded parameters in the forcefield
> > >
> > > On Wednesday, September 9, 2015, Justin Lemkul 
> wrote:
> > >
> > > >
> > > >
> > > > On 9/9/15 7:29 AM, Maryam Kowsar wrote:
> > > >
> > > >> Hi dan
> > > >> I think that's not possible to change forcefield parameters and use
> > the
> > > >> old
> > > >> defined forcefield like opls. When you change the parameters in .itp
> > you
> > > >> should introduce your own forcefield. Try to have all the needed
> files
> > > of
> > > >> forcefield in a new folder and use that during making topology.
> > > >>
> > > >>
> > > > This is not true. Any force field can be modified or extended. A
> local
> > > > copy of a modified force field is a safe recommendation, but in the
> > case
> > > of
> > > > simply adding new atom types, there's little harm that can be done.
> > > >
> > > > -Justin
> > > >
> > > > On Tuesday, September 8, 2015, Phwey Gil  wrote:
> > > >>
> > > >> Hi,
> > > >>>
> > > >>> I am looking to specify my own parameters for LJ parameters. Using
> > the
> > > >>> OPLS
> > > >>> forcefield, I only want to change the LJ parameters of some atoms.
> > > >>>
> > > >>> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
> > > >>> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I
> want
> > to
> > > >>> change the LJ parameters for the hydrogens in C8H16O2 only.
> > > >>>
> > > >>> I have tried specifying [ atomtypes ] in various places (In .top or
> > > .itp)
> > > >>> using the following format:
> > > >>>
> > > >>>   [ atomtypes ]
> > > >>>H H  1.008  0.450 A   5.66387665E-4
> > > >>> 2.80730518E-7
> > > >>>
> > > >>> But I was not successful; I checked topol.tpr and the numbers are
> > > >>> according
> > > >>> to OPLS and not my specified values.
> > > >>>
> > > >>> Can someone give me advice on how to do this? I've checked the
> forums
> > > >>> and I
> > > >>> was not successful at 

Re: [gmx-users] Does .xtc enough for all kind of analysis?

[Chandan Choudhury]

trr also contains velocities and forces.

Chandan

On Thu, Sep 10, 2015 at 11:18 AM, Tushar Ranjan Moharana <
tusharranjanmohar...@gmail.com> wrote:

> Hi everyone,
> Just has a general doubt. Does compressed coordinate file (.xtc) enough for
> all kind of analysis? If so then why we need a large .trr file? Is there
> any difference in quality of the data or performance during analysis?
>
>
> Thanks a lot, in advance, for your answer.
>
>
> "A society with free knowledge is better than a society with free food"
>
> Tushar Ranjan Moharana
> B. Tech, NIT Warangal
> Ph D Student, CCMB
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 

Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India

*"All work and no play makes Jack a dull boy...”*
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[gmx-users] Does .xtc enough for all kind of analysis?

[Tushar Ranjan Moharana]

Hi everyone,
Just has a general doubt. Does compressed coordinate file (.xtc) enough for
all kind of analysis? If so then why we need a large .trr file? Is there
any difference in quality of the data or performance during analysis?


Thanks a lot, in advance, for your answer.


"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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Re: [gmx-users] User-Specified LJ Epsilon and Sigma

[Mark Abraham]

Hi,

On Wed, Sep 9, 2015 at 7:55 PM Phwey Gil  wrote:

> Hi Justin, Maryam,
>
> My initial problem was that I did not specify the atom types as Justin
> said. Now I am able to change the masses and charges easily, but there are
> still some problems with implementing the lennard-jones potential.
>
> In my .itp file I write:
>  [ atomtypes ]
>  X  1  7.777  0.450  A  2  3
>
> Where X is the atom in question, and I have made up numbers to see how they
> appear in topol.tpr. I was able to see that the masses and charges can be
> implemented straightforwardly. However, the C6 and C12 parameters are not
> (2 and 3). The output values found in topol.tpr are:
>
>  functype[9]=LJ_SR, c6= 1.41771114e+00, c12= 3.59777004e-01
>

LJ parameters for the two atom types involved in an interaction combine
according to the equations in chapter 4 of the manual. There's been some
pre-computation already.

Additionally, [ Bonds ] do not appear in the topol.tpr either.
>

Well, don't ask grompp to convert your bonds into constraints ;-)

Mark


> On Wed, Sep 9, 2015 at 7:43 AM, Maryam Kowsar 
> wrote:
>
> > Hi justin
> > Actually i modified the forcefield parameters to introduce atoms that are
> > not present in that. I think you are right in the case that we want to
> > change bonded or nonbonded parameters in the forcefield
> >
> > On Wednesday, September 9, 2015, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 9/9/15 7:29 AM, Maryam Kowsar wrote:
> > >
> > >> Hi dan
> > >> I think that's not possible to change forcefield parameters and use
> the
> > >> old
> > >> defined forcefield like opls. When you change the parameters in .itp
> you
> > >> should introduce your own forcefield. Try to have all the needed files
> > of
> > >> forcefield in a new folder and use that during making topology.
> > >>
> > >>
> > > This is not true. Any force field can be modified or extended. A local
> > > copy of a modified force field is a safe recommendation, but in the
> case
> > of
> > > simply adding new atom types, there's little harm that can be done.
> > >
> > > -Justin
> > >
> > > On Tuesday, September 8, 2015, Phwey Gil  wrote:
> > >>
> > >> Hi,
> > >>>
> > >>> I am looking to specify my own parameters for LJ parameters. Using
> the
> > >>> OPLS
> > >>> forcefield, I only want to change the LJ parameters of some atoms.
> > >>>
> > >>> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
> > >>> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want
> to
> > >>> change the LJ parameters for the hydrogens in C8H16O2 only.
> > >>>
> > >>> I have tried specifying [ atomtypes ] in various places (In .top or
> > .itp)
> > >>> using the following format:
> > >>>
> > >>>   [ atomtypes ]
> > >>>H H  1.008  0.450 A   5.66387665E-4
> > >>> 2.80730518E-7
> > >>>
> > >>> But I was not successful; I checked topol.tpr and the numbers are
> > >>> according
> > >>> to OPLS and not my specified values.
> > >>>
> > >>> Can someone give me advice on how to do this? I've checked the forums
> > >>> and I
> > >>> was not successful at finding the correct information.
> > >>>
> > >>> Best Regards,
> > >>>
> > >>> Dan
> > >>>
> > >>> --
> > >>> Dan Gil
> > >>> Case Western Reserve University | Class of 2016
> > >>> Researcher, Department of Chemical Engineering
> > >>> ps...@case.edu 
> > >>> --
> > >>> 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 .
> > >>>
> > >>>
> > > --
> > > ==
> > >
> > > 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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> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > 

Re: [gmx-users] User-Specified LJ Epsilon and Sigma

[Phwey Gil]

Hi Justin, Maryam,

My initial problem was that I did not specify the atom types as Justin
said. Now I am able to change the masses and charges easily, but there are
still some problems with implementing the lennard-jones potential.

In my .itp file I write:
 [ atomtypes ]
 X  1  7.777  0.450  A  2  3

Where X is the atom in question, and I have made up numbers to see how they
appear in topol.tpr. I was able to see that the masses and charges can be
implemented straightforwardly. However, the C6 and C12 parameters are not
(2 and 3). The output values found in topol.tpr are:

 functype[9]=LJ_SR, c6= 1.41771114e+00, c12= 3.59777004e-01

Additionally, [ Bonds ] do not appear in the topol.tpr either.



On Wed, Sep 9, 2015 at 7:43 AM, Maryam Kowsar 
wrote:

> Hi justin
> Actually i modified the forcefield parameters to introduce atoms that are
> not present in that. I think you are right in the case that we want to
> change bonded or nonbonded parameters in the forcefield
>
> On Wednesday, September 9, 2015, Justin Lemkul  wrote:
>
> >
> >
> > On 9/9/15 7:29 AM, Maryam Kowsar wrote:
> >
> >> Hi dan
> >> I think that's not possible to change forcefield parameters and use the
> >> old
> >> defined forcefield like opls. When you change the parameters in .itp you
> >> should introduce your own forcefield. Try to have all the needed files
> of
> >> forcefield in a new folder and use that during making topology.
> >>
> >>
> > This is not true. Any force field can be modified or extended. A local
> > copy of a modified force field is a safe recommendation, but in the case
> of
> > simply adding new atom types, there's little harm that can be done.
> >
> > -Justin
> >
> > On Tuesday, September 8, 2015, Phwey Gil  wrote:
> >>
> >> Hi,
> >>>
> >>> I am looking to specify my own parameters for LJ parameters. Using the
> >>> OPLS
> >>> forcefield, I only want to change the LJ parameters of some atoms.
> >>>
> >>> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
> >>> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
> >>> change the LJ parameters for the hydrogens in C8H16O2 only.
> >>>
> >>> I have tried specifying [ atomtypes ] in various places (In .top or
> .itp)
> >>> using the following format:
> >>>
> >>>   [ atomtypes ]
> >>>H H  1.008  0.450 A   5.66387665E-4
> >>> 2.80730518E-7
> >>>
> >>> But I was not successful; I checked topol.tpr and the numbers are
> >>> according
> >>> to OPLS and not my specified values.
> >>>
> >>> Can someone give me advice on how to do this? I've checked the forums
> >>> and I
> >>> was not successful at finding the correct information.
> >>>
> >>> Best Regards,
> >>>
> >>> Dan
> >>>
> >>> --
> >>> Dan Gil
> >>> Case Western Reserve University | Class of 2016
> >>> Researcher, Department of Chemical Engineering
> >>> ps...@case.edu 
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> >>> posting!
> >>>
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> >>>
> >>>
> > --
> > ==
> >
> > 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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-- 
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
ps...@case.edu
-- 
Gromacs Users mailing list

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