Re: [gmx-users] Aggregation or phase separation

[gozde ergin]

Dear Dr. Warren;

Is there any publication that I can read?
Also could you please give me hint how to define the phase of aggregates in 
water by using Gromacs tool?
My PhD defence is in two weeks and I would like to answer if get any question :)

Bests
> On 09 Oct 2017, at 23:16, Dallas Warren <dallas.war...@monash.edu> wrote:
> 
> There isn't really anything currently.
> 
> It is an issue we deal with, have a few things currently do that are
> published. Have another in the works.
> Catch ya,
> 
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a 
> nail.
> 
> 
> On 10 October 2017 at 01:08, gozde ergin <gozdeeer...@gmail.com> wrote:
>> I am using Gromacs to study the cis-pinonic acid aggregation in water.
>> In order to use the Gibbs-duhem relation, I would like to know if these 
>> aggregates form inside the water are pseudo-phase or separate phase?
>> Do you have any hint how to define the phase of aggregates in water by using 
>> Gromacs tool?
>> 
>> Thanks in advance.
>> --
>> Gromacs Users mailing list
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[gmx-users] Aggregation or phase separation

[gozde ergin]

I am using Gromacs to study the cis-pinonic acid aggregation in water.
In order to use the Gibbs-duhem relation, I would like to know if these 
aggregates form inside the water are pseudo-phase or separate phase?
Do you have any hint how to define the phase of aggregates in water by using 
Gromacs tool?

Thanks in advance.
-- 
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[gmx-users] Differentiate of aggregation of precipitation in MD simulation

[gozde ergin]

Dear all,

I am simulation the aggregation of HULIS like molecule. 
However I would like know if there is way in Gromacs to analyse if these bunch 
of molecules gather together because 
of aggregation or precipitation?

Bests
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[gmx-users] Display error bars for traj

[gozde ergin]

Dear all,

I use g_traj command to extract the z-coordinate of the molecules from .xtc 
files.
I wonder is there a way to display also the error bars for these coordinates?

Bests
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Re: [gmx-users] units of gmx wham output

[gozde ergin]

Capital {S-1} is to make it  ^{-1}. It is for superscript. And the \N returns 
the text to the default state.
So it is basically the y-axis name for xmgrace tool. 
If you plot your .xvg file by using xmgrace you will see kj/mol on your Y-axis 
title.

Overall your energy unit is kj/mol which is what you asked for.


> On 27 Jul 2017, at 16:54, Irem Altan  wrote:
> 
> (kJ mol\S-1\N)

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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Thank Justin.
Mark you are right. I did not think about to check the manual. 

Thanks again.
> On 22 Jun 2017, at 15:51, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> 
> Hi,
> 
> I'd start by looking in the documentation. Section 5.3.2 of the manual
> clearly suggests putting it in the ffnonbonded.itp file, which is where you
> expected to find it at the start of this thread, right? :-)
> 
> Mark
> 
> On Thu, Jun 22, 2017 at 3:47 PM gozde ergin <gozdeeer...@gmail.com 
> <mailto:gozdeeer...@gmail.com>> wrote:
> 
>> Hey Justin,
>> 
>> I figured out how they calculated the sigma values.
>> Basically they just take the geometric mean of nitrogen and oxygen sigma
>> and epsilon from ffnonbed.itp file in OPLS-AA force field
>> and calculated the pairwise LJ for N-O interaction.
>> 
>> Now I also try to add this information in my topol.top file.
>> In order to do that as you have mentioned I added a section ,
>> 
>> [ nonbond_params ]
>> ; i j   funcsigma   epsilon
>> opls_287  opls_272  1  0.323161248385416  0.790543521382599
>> 
>> 
>> after [ atoms ] section however I am facing with an error :
>> 
>> Fatal error:
>> Syntax error - File topol.top, line 42
>> Last line read:
>> '[ nonbond_params ]'
>> Invalid order for directive nonbond_params
>> 
>> Any suggestion would be appreciated.
>> 
>>> On 21 Jun 2017, at 16:46, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 6/21/17 10:39 AM, gozde ergin wrote:
>>>> Hi MArk,
>>>> Thanks for the respond. I understood that point however I still do not
>> get which sigma to change.
>>>> I the paper JCTC 2017, Miller et. al. they have mentioned that they
>> increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>>>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
>> notrogen and one for carboxylate oxygen.
>>>> 
>>   sigmaepsilon
>>>> opls_287   N3   7  14.00670-0.300   A3.25000e-01
>> 7.11280e-01
>>>> opls_272   O2   8  15.99940-0.800   A2.96000e-01
>> 8.78640e-01
>>>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>>>> Which sigma should I change?
>>> 
>>> What people are doing more and more is introducing pair-specific
>> parameters to override the combination rule values.  That's likely what is
>> being referred to. OPLS-AA by default does not use pair-specific LJ
>> interactions, hence why you find no [nonbond_params] in ffnonbonded.itp.
>> The same is true of AMBER.  CHARMM uses some (also called NBFIX in the
>> literature), while GROMOS uses a ton of these.
>>> 
>>> To override the LJ combination rules, add a [nonbond_params] directive
>> with the published parameters, which refer to an *interaction*, not an atom
>> type.
>>> 
>>> -Justin
>>> 
>>>> Thanks
>>>>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abra...@gmail.com>
>> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Different force fields work differently and thus are implemented
>>>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
>> sigma
>>>>> is a property of the atomtype
>>>>> 
>>>>> Mark
>>>>> 
>>>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com>
>> wrote:
>>>>> 
>>>>>> Dear users,
>>>>>> 
>>>>>> I am trying to change the sigma value of amino nitrogen–carboxylate
>> oxygen
>>>>>> interactions in OPLSAA in GROMACS.
>>>>>> However I have difficulties to understand which parameter i should
>> change
>>>>>> in ffnonbonded.itp file?
>>>>>> I am looking something like [ nonbond_params ] section however it is
>> not
>>>>>> exist in ffnonbonded.itp?
>>>>>> Any help would be appreciated.
>>>>>> 
>>>>>> Thanks in advance.
>>>>>> --
>>>>>> 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/Mailin

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Hey Justin,

I figured out how they calculated the sigma values. 
Basically they just take the geometric mean of nitrogen and oxygen sigma and 
epsilon from ffnonbed.itp file in OPLS-AA force field 
and calculated the pairwise LJ for N-O interaction.

Now I also try to add this information in my topol.top file. 
In order to do that as you have mentioned I added a section ,

[ nonbond_params ]
; i j   funcsigma   epsilon
opls_287  opls_272  1  0.323161248385416  0.790543521382599


after [ atoms ] section however I am facing with an error :

Fatal error:
Syntax error - File topol.top, line 42
Last line read:
'[ nonbond_params ]'
Invalid order for directive nonbond_params

Any suggestion would be appreciated.

> On 21 Jun 2017, at 16:46, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 6/21/17 10:39 AM, gozde ergin wrote:
>> Hi MArk,
>> Thanks for the respond. I understood that point however I still do not get 
>> which sigma to change.
>> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
>> the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino 
>> notrogen and one for carboxylate oxygen.
>>  
>>  sigmaepsilon
>>  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
>>  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01
>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>> Which sigma should I change?
> 
> What people are doing more and more is introducing pair-specific parameters 
> to override the combination rule values.  That's likely what is being 
> referred to. OPLS-AA by default does not use pair-specific LJ interactions, 
> hence why you find no [nonbond_params] in ffnonbonded.itp.  The same is true 
> of AMBER.  CHARMM uses some (also called NBFIX in the literature), while 
> GROMOS uses a ton of these.
> 
> To override the LJ combination rules, add a [nonbond_params] directive with 
> the published parameters, which refer to an *interaction*, not an atom type.
> 
> -Justin
> 
>> Thanks
>>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abra...@gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> Different force fields work differently and thus are implemented
>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
>>> is a property of the atomtype
>>> 
>>> Mark
>>> 
>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com> wrote:
>>> 
>>>> Dear users,
>>>> 
>>>> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
>>>> interactions in OPLSAA in GROMACS.
>>>> However I have difficulties to understand which parameter i should change
>>>> in ffnonbonded.itp file?
>>>> I am looking something like [ nonbond_params ] section however it is not
>>>> exist in ffnonbonded.itp?
>>>> Any help would be appreciated.
>>>> 
>>>> Thanks in advance.
>>>> --
>>>> 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.
>>> -- 
>>> 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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <ht

Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

However in the paper they have mentioned that they increased the sigma  for 
amino nitrogen–carboxylate oxygen interactions 
by 0.13Angstrom   relative to the original value.
So I assume there should be original value? 
However you mentioned that there is no pair-specific LJ interaction in OPLSAA. 
Even if I add a [nonbond_params] what epsilon and sigma should I use? Because 
they talk about the increment in sigma and I do not know the original value.
Maybe I should connect them directly.

Thanks Justin.

> On 21 Jun 2017, at 16:46, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 6/21/17 10:39 AM, gozde ergin wrote:
>> Hi MArk,
>> Thanks for the respond. I understood that point however I still do not get 
>> which sigma to change.
>> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
>> the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino 
>> notrogen and one for carboxylate oxygen.
>>  
>>  sigmaepsilon
>>  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
>>  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01
>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>> Which sigma should I change?
> 
> What people are doing more and more is introducing pair-specific parameters 
> to override the combination rule values.  That's likely what is being 
> referred to. OPLS-AA by default does not use pair-specific LJ interactions, 
> hence why you find no [nonbond_params] in ffnonbonded.itp.  The same is true 
> of AMBER.  CHARMM uses some (also called NBFIX in the literature), while 
> GROMOS uses a ton of these.
> 
> To override the LJ combination rules, add a [nonbond_params] directive with 
> the published parameters, which refer to an *interaction*, not an atom type.
> 
> -Justin
> 
>> Thanks
>>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abra...@gmail.com> wrote:
>>> 
>>> Hi,
>>> 
>>> Different force fields work differently and thus are implemented
>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
>>> is a property of the atomtype
>>> 
>>> Mark
>>> 
>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com> wrote:
>>> 
>>>> Dear users,
>>>> 
>>>> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
>>>> interactions in OPLSAA in GROMACS.
>>>> However I have difficulties to understand which parameter i should change
>>>> in ffnonbonded.itp file?
>>>> I am looking something like [ nonbond_params ] section however it is not
>>>> exist in ffnonbonded.itp?
>>>> Any help would be appreciated.
>>>> 
>>>> Thanks in advance.
>>>> --
>>>> 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.
>>> -- 
>>> 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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>>> 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
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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Hi MArk,

Thanks for the respond. I understood that point however I still do not get 
which sigma to change.
I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
the for nitrogen–carboxylate oxygen interactions in OPLSAA.
However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino notrogen 
and one for carboxylate oxygen.

  
sigmaepsilon
 opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
 opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01

Which one defines the amino nitrogen–carboxylate oxygen interactions?
Which sigma should I change?

Thanks
> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> 
> Hi,
> 
> Different force fields work differently and thus are implemented
> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
> is a property of the atomtype
> 
> Mark
> 
> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com> wrote:
> 
>> Dear users,
>> 
>> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
>> interactions in OPLSAA in GROMACS.
>> However I have difficulties to understand which parameter i should change
>> in ffnonbonded.itp file?
>> I am looking something like [ nonbond_params ] section however it is not
>> exist in ffnonbonded.itp?
>> Any help would be appreciated.
>> 
>> Thanks in advance.
>> --
>> 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.
> -- 
> 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] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Dear users,

I am trying to change the sigma value of amino nitrogen–carboxylate oxygen 
interactions in OPLSAA in GROMACS.
However I have difficulties to understand which parameter i should change in 
ffnonbonded.itp file?
I am looking something like [ nonbond_params ] section however it is not exist 
in ffnonbonded.itp?
Any help would be appreciated.

Thanks in advance.
-- 
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] extract the coordinate by using traj command for sphere system

[gozde ergin]

Thanks Justin !
> On 12 Jun 2017, at 14:01, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 6/12/17 7:59 AM, gozde ergin wrote:
>> But I need to understand if atoms go beyond the wall (flat-bottom restraint).
>> In order to understant that I need to know their coordinate with respect to 
>> radius.
>> Do you think I should use the basic math here :  r = (x^2 + y^2 + z^2)^(1/2) 
>> ?
> 
> Yes, you still need to consider the individual (x,y,z) of each restrained 
> atom. A COM selection does you no good.  You'll have to determine the 
> displacement of each atom from the reference position of the restraint 
> potential.
> 
> -Justin
> 
>>> On 12 Jun 2017, at 13:55, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 6/12/17 4:36 AM, gozde ergin wrote:
>>>> Dear all,
>>>> In order to calculate the osmotic pressure I would like to extract the 
>>>> coordinate of my atoms by using g_traj command.
>>>> Before my box was cubic and by using
>>>> gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -nox 
>>>> -noy
>>>> I was getting coordinate of all of my atoms in the system. So this was 
>>>> working fine.
>>>> However now my system is sphere and I again want to extract the coordinate 
>>>> file of all my atom. However if I use:
>>>> gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -com
>>>> I only get the coordinate X,Y and Z component not all atoms coordinates.
>>> 
>>> Because you're doing something totally different here than in the command 
>>> above.  Here, you're asking for (x,y,z) coordinates of the COM of the 
>>> selection.
>>> 
>>>> Do you have any hint how to extract the atoms coordinate files in gromacs 
>>>> for sphere system?
>>> 
>>> It's no different than any system.  Use gmx traj as you did in the first 
>>> command, with a proper selection.  Geometry of the system is irrelevant.
>>> 
>>> -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
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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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==
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Re: [gmx-users] extract the coordinate by using traj command for sphere system

[gozde ergin]

But I need to understand if atoms go beyond the wall (flat-bottom restraint). 

In order to understant that I need to know their coordinate with respect to 
radius. 

Do you think I should use the basic math here :  r = (x^2 + y^2 + z^2)^(1/2) ?


> On 12 Jun 2017, at 13:55, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 6/12/17 4:36 AM, gozde ergin wrote:
>> Dear all,
>> In order to calculate the osmotic pressure I would like to extract the 
>> coordinate of my atoms by using g_traj command.
>> Before my box was cubic and by using
>> gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -nox -noy
>> I was getting coordinate of all of my atoms in the system. So this was 
>> working fine.
>> However now my system is sphere and I again want to extract the coordinate 
>> file of all my atom. However if I use:
>> gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -com
>> I only get the coordinate X,Y and Z component not all atoms coordinates.
> 
> Because you're doing something totally different here than in the command 
> above.  Here, you're asking for (x,y,z) coordinates of the COM of the 
> selection.
> 
>> Do you have any hint how to extract the atoms coordinate files in gromacs 
>> for sphere system?
> 
> It's no different than any system.  Use gmx traj as you did in the first 
> command, with a proper selection.  Geometry of the system is irrelevant.
> 
> -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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[gmx-users] extract the coordinate by using traj command for sphere system

[gozde ergin]

Dear all,

In order to calculate the osmotic pressure I would like to extract the 
coordinate of my atoms by using g_traj command. 

Before my box was cubic and by using

gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -nox -noy

I was getting coordinate of all of my atoms in the system. So this was working 
fine.

However now my system is sphere and I again want to extract the coordinate file 
of all my atom. However if I use: 

gmx_mpi traj -f nvt.trr -s nvt.tpr -n index.ndx -ox coord-atoms.xvg -com

I only get the coordinate X,Y and Z component not all atoms coordinates.

Do you have any hint how to extract the atoms coordinate files in gromacs for 
sphere system?

Thanks in advance.


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Re: [gmx-users] powercut command

[gozde ergin]

Lincs warning usually occurs for the system that not minimized.
You can try to minimize your system before running the real simulation.

Other option would be use -maxwarn flag but please use it only if you know that 
these warnings are not important. 


> On 13 Apr 2017, at 11:10, Anshul Lahariya  wrote:
> 
> This is a error that i got during mdrun. plzzz help..
> 
> 
> 
> Program: gmx mdrun, version 2016.2
> Source file: src/gromacs/mdlib/constr.cpp (line 167)
> 
> Fatal error:
> Too many LINCS warnings (1000)
> If you know what you are doing you can adjust the lincs warning threshold in
> your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> 
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> [root@dhcppc58 AhpE_MSH]# Program: gmx mdrun, version 2016.2
> 
> 
> On Thu, Apr 13, 2017 at 12:06 PM, Anshul Lahariya <
> anshullahariy...@gmail.com> wrote:
> 
>> Thank u so much
>> 
>> #Devashish Das
>> 
>> 
>> On Thu, Apr 13, 2017 at 11:30 AM, Devashish_Das >> wrote:
>> 
>>> Please use to resume:
>>> 
>>> gmx mdrun -v -deffnm 10ns -cpi 10ns.cpt
>>> 
>>> 
>>> 
>>> 
>>> On Thu, Apr 13, 2017 at 11:12 AM, Anshul Lahariya <
>>> anshullahariy...@gmail.com> wrote:
>>> 
 My md was running. Suddenly power supply was cuts due to some reason
>>> and my
 my MD stops..
 To continue my MD, I use command:-
 
 
 gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi 10ns.cpt
 -cpo 10ns.cpt -append
 
 
 
 but shows error.
 
 
 Error in user input:
 Invalid command-line options
Unknown command-line option -md_1_0.xtc
 
 For more information and tips for troubleshooting, please check the
>>> GROMACS
 website at http://www.gromacs.org/Documentation/Errors
 ---
 [root@dhcppc58 AhpE_MSH]#
 
 
 
 Plzz.. help me out
 --
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>>> 
>>> 
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>>> 
>>> Regards,
>>> 
>>> Devashish Das
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>> 
>> 
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Re: [gmx-users] Replica Exchange for surface tension

[gozde ergin]

Hi Justin,

I found a new optimized NBFIX parameter for SOD-Oxygen of Betaine and 
SOD-Oxygen of SDS. 
On the other hand since betaine is a zwitterionic molecule there is + charge on 
Nitrogen(N) and - charge on the Oxygen atoms and SDS is anionic there is - 
charge on SO4 and there is + SOD molecules inside the bulk, I also need to 
define NBFIX parameter between N-Oxygen of betaine and N-Oxygen of SDS. 
However I could not find them, do you have any hint how to develop new 
optimised NBFIX parameter these specific combination? 
There is  2016 JCTC Yoo et.al. paper that did some optimization however they 
used amine groups and betaine has tetramethylamine group.

Thanks in advance.



> 
> 
> 
> On 3/28/17 2:59 PM, gozde ergin wrote:
>> I use Charmm36 force field. Do you mean the force field parameter between
>> cocobetaine and SDS? Because for pure surfactant I am able to estimate the
>> correct surface tension. Which means force field parameter of SDS-water and
>> cocobetaine-water is fine.
>> 
> 
> SDS is a standard part of CHARMM36 but I have no idea what cocobetaine is.  
> Did you find existing parameters for it or did you do the parametrization 
> yourself? The larger point is that you've probably stumbled upon the corner 
> cases that often come up - some combination of parameters has never been 
> looked at before and it requires more refinement.  If both interact with 
> water fine but interact with each other improperly, that means either the 
> SDS-cocobetaine interactions are too weak or too strong, or that they induce 
> some sort of abnormal conformational sampling.
> 
> You'll need to look at the microscopic details of how they interact - which 
> groups are associated with which, how the conformational ensembles of each 
> differ from those observed in water, etc.  Then you can focus on specific 
> elements of refinement that may need to be done (e.g. NBFIX for LJ 
> interactions that are often the culprit in such cases, and/or perhaps some 
> sub-par dihedral parameters that lead to bad sampling when a particular 
> interaction occurs).
> 
> -Justin
> 
>> Sent from my iPhone
>> 
>>> On 28 Mar 2017, at 7:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>>> On 3/28/17 12:43 PM, gozde ergin wrote: I have a mixed system of SDS and
>>>> cocobetaine on water surface. I estimated the surface tension of SDS on
>>>> water surface and cocabetaine on surface tension separately and correctly
>>>> (comparing with experimental results). However I could not estimate the
>>>> correct surface tension for SDS-cocobetaine mix in even 150 ns
>>>> simulation. Do you think replica exchange simulation would help me to
>>>> estimate the correct surface tension of mixed system? Do you have any
>>>> idea why I failed in estimating the mixed system surface tension?
>>>> 
>>> 
>>> If a physical model fails to produce known physical properties, the problem
>>> is often the model itself.  I'd suspect the force field parameters first.
>>> What is the source of your parameters?
>>> 
>>> Replica exchange helps you get over large barriers to improve sampling, but
>>> I doubt that's useful here in a mixture of small molecules.
>>> 
>>> -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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> 
> -- 
> ==
> 
> 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 2

Re: [gmx-users] Replica Exchange for surface tension

[gozde ergin]

Justin what would you suggest if I simulate the system under constant surface 
tension since I know the correct surface tension from experiments.
Can I get some information about the force field quality if I compare the 
conformation of the surface under constant surface tension (N\gammaT) and under 
NVT ensemble?
 
> On 29 Mar 2017, at 15:21, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Exactly SDS is CHARMM36 but cocobetaine not.
> 
>> On 29 Mar 2017, at 15:18, Justin Lemkul <jalem...@vt.edu 
>> <mailto:jalem...@vt.edu>> wrote:
>> 
>> 
>> 
>> On 3/29/17 9:16 AM, gozde ergin wrote:
>>> Are you sure it is not CHARMM36 because it is written:
>>> 
>>> ;;
>>> ;; Generated by CHARMM-GUI (http://www.charmm-gui.org 
>>> <http://www.charmm-gui.org/>) v1.7
>>> ;;
>>> ;; psf2itp.py
>>> ;;
>>> ;; Correspondance:
>>> ;; j712l...@ku.edu <mailto:j712l...@ku.edu> or won...@ku.edu 
>>> <mailto:won...@ku.edu>
>>> ;;
>>> ;; CHARMM36 FF in GROMACS format
>>> ;;
>>> 
>>> on the top of the .itp files.
>>> 
>> 
>> OK, I was thinking too quickly, the workflow goes like this: If a molecule 
>> is identified as part of the existing force field, it is used.  If it is 
>> not, then CGenFF is called.  So your SDS may be CHARMM36 but your 
>> cocobetaine is not. You can check against the CHARMM force field files and 
>> also the atom types themselves.  If the second character is "G" then it is 
>> CGenFF, otherwise it is stock CHARMM.
>> 
>> Do not rely on header comments; those are often boilerplate.  Check the 
>> parameters themselves.
>> 
>> -Justin
>> 
>>> 
>>> 
>>>> On 29 Mar 2017, at 15:06, Justin Lemkul <jalem...@vt.edu 
>>>> <mailto:jalem...@vt.edu>> wrote:
>>>> 
>>>> 
>>>> 
>>>> On 3/29/17 4:15 AM, gozde ergin wrote:
>>>>> I used CHARMM GUI Input Generator tool both for SDS and cocobetaine.
>>>> 
>>>> For the sake of clarity, you should understand that you are *not* then 
>>>> using CHARMM36.  CHARMM-GUI calls the CGenFF program to parametrize the 
>>>> molecule, so you are using CGenFF parameters, which are compatible with 
>>>> CHARMM by design, but are not the standard CHARMM36 parameters.  Thus your 
>>>> SDS model will differ from the standard one that we have in the 
>>>> lipids/detergents file.  You should compare it to make sure it is 
>>>> reasonable.  A general force field will sacrifice some accuracy in the 
>>>> name of generality and transferability.
>>>> 
>>>>> So basically the reason of not getting correct surface tension is bad 
>>>>> parametrisation of force field.
>>>>> Then I should not spend time on simulation the replica exchange.
>>>> 
>>>> Indeed.  Look at the things I mentioned before.  If the model doesn't work 
>>>> well, then you have to get into the details of why.  Burning through more 
>>>> time hoping it will work out and expensive stuff like REMD is just a waste.
>>>> 
>>>> -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 
>>>> <mailto:jalem...@outerbanks.umaryland.edu> | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul 
>>>> <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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>>>> a mail to gmx-users-requ...@gromacs.org.
>>> 
>> 
>> -- 
>> ===

Re: [gmx-users] Replica Exchange for surface tension

[gozde ergin]

Exactly SDS is CHARMM36 but cocobetaine not.

> On 29 Mar 2017, at 15:18, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 3/29/17 9:16 AM, gozde ergin wrote:
>> Are you sure it is not CHARMM36 because it is written:
>> 
>> ;;
>> ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
>> ;;
>> ;; psf2itp.py
>> ;;
>> ;; Correspondance:
>> ;; j712l...@ku.edu or won...@ku.edu
>> ;;
>> ;; CHARMM36 FF in GROMACS format
>> ;;
>> 
>> on the top of the .itp files.
>> 
> 
> OK, I was thinking too quickly, the workflow goes like this: If a molecule is 
> identified as part of the existing force field, it is used.  If it is not, 
> then CGenFF is called.  So your SDS may be CHARMM36 but your cocobetaine is 
> not. You can check against the CHARMM force field files and also the atom 
> types themselves.  If the second character is "G" then it is CGenFF, 
> otherwise it is stock CHARMM.
> 
> Do not rely on header comments; those are often boilerplate.  Check the 
> parameters themselves.
> 
> -Justin
> 
>> 
>> 
>>> On 29 Mar 2017, at 15:06, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 3/29/17 4:15 AM, gozde ergin wrote:
>>>> I used CHARMM GUI Input Generator tool both for SDS and cocobetaine.
>>> 
>>> For the sake of clarity, you should understand that you are *not* then 
>>> using CHARMM36.  CHARMM-GUI calls the CGenFF program to parametrize the 
>>> molecule, so you are using CGenFF parameters, which are compatible with 
>>> CHARMM by design, but are not the standard CHARMM36 parameters.  Thus your 
>>> SDS model will differ from the standard one that we have in the 
>>> lipids/detergents file.  You should compare it to make sure it is 
>>> reasonable.  A general force field will sacrifice some accuracy in the name 
>>> of generality and transferability.
>>> 
>>>> So basically the reason of not getting correct surface tension is bad 
>>>> parametrisation of force field.
>>>> Then I should not spend time on simulation the replica exchange.
>>> 
>>> Indeed.  Look at the things I mentioned before.  If the model doesn't work 
>>> well, then you have to get into the details of why.  Burning through more 
>>> time hoping it will work out and expensive stuff like REMD is just a waste.
>>> 
>>> -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.
>> 
> 
> -- 
> ==
> 
> 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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==
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Re: [gmx-users] Replica Exchange for surface tension

[gozde ergin]

Are you sure it is not CHARMM36 because it is written:

;;
;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
;;
;; psf2itp.py
;;
;; Correspondance:
;; j712l...@ku.edu or won...@ku.edu
;;
;; CHARMM36 FF in GROMACS format
;;

on the top of the .itp files.



> On 29 Mar 2017, at 15:06, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 3/29/17 4:15 AM, gozde ergin wrote:
>> I used CHARMM GUI Input Generator tool both for SDS and cocobetaine.
> 
> For the sake of clarity, you should understand that you are *not* then using 
> CHARMM36.  CHARMM-GUI calls the CGenFF program to parametrize the molecule, 
> so you are using CGenFF parameters, which are compatible with CHARMM by 
> design, but are not the standard CHARMM36 parameters.  Thus your SDS model 
> will differ from the standard one that we have in the lipids/detergents file. 
>  You should compare it to make sure it is reasonable.  A general force field 
> will sacrifice some accuracy in the name of generality and transferability.
> 
>> So basically the reason of not getting correct surface tension is bad 
>> parametrisation of force field.
>> Then I should not spend time on simulation the replica exchange.
> 
> Indeed.  Look at the things I mentioned before.  If the model doesn't work 
> well, then you have to get into the details of why.  Burning through more 
> time hoping it will work out and expensive stuff like REMD is just a waste.
> 
> -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
> 
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> http://mackerell.umaryland.edu/~jalemkul
> 
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Re: [gmx-users] Replica Exchange for surface tension

[gozde ergin]

I used CHARMM GUI Input Generator tool both for SDS and cocobetaine. 
So basically the reason of not getting correct surface tension is bad 
parametrisation of force field.
Then I should not spend time on simulation the replica exchange.

Thanks Justin.

> On 28 Mar 2017, at 22:48, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 3/28/17 2:59 PM, gozde ergin wrote:
>> I use Charmm36 force field. Do you mean the force field parameter between
>> cocobetaine and SDS? Because for pure surfactant I am able to estimate the
>> correct surface tension. Which means force field parameter of SDS-water and
>> cocobetaine-water is fine.
>> 
> 
> SDS is a standard part of CHARMM36 but I have no idea what cocobetaine is.  
> Did you find existing parameters for it or did you do the parametrization 
> yourself? The larger point is that you've probably stumbled upon the corner 
> cases that often come up - some combination of parameters has never been 
> looked at before and it requires more refinement.  If both interact with 
> water fine but interact with each other improperly, that means either the 
> SDS-cocobetaine interactions are too weak or too strong, or that they induce 
> some sort of abnormal conformational sampling.
> 
> You'll need to look at the microscopic details of how they interact - which 
> groups are associated with which, how the conformational ensembles of each 
> differ from those observed in water, etc.  Then you can focus on specific 
> elements of refinement that may need to be done (e.g. NBFIX for LJ 
> interactions that are often the culprit in such cases, and/or perhaps some 
> sub-par dihedral parameters that lead to bad sampling when a particular 
> interaction occurs).
> 
> -Justin
> 
>> Sent from my iPhone
>> 
>>> On 28 Mar 2017, at 7:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>>> On 3/28/17 12:43 PM, gozde ergin wrote: I have a mixed system of SDS and
>>>> cocobetaine on water surface. I estimated the surface tension of SDS on
>>>> water surface and cocabetaine on surface tension separately and correctly
>>>> (comparing with experimental results). However I could not estimate the
>>>> correct surface tension for SDS-cocobetaine mix in even 150 ns
>>>> simulation. Do you think replica exchange simulation would help me to
>>>> estimate the correct surface tension of mixed system? Do you have any
>>>> idea why I failed in estimating the mixed system surface tension?
>>>> 
>>> 
>>> If a physical model fails to produce known physical properties, the problem
>>> is often the model itself.  I'd suspect the force field parameters first.
>>> What is the source of your parameters?
>>> 
>>> Replica exchange helps you get over large barriers to improve sampling, but
>>> I doubt that's useful here in a mixture of small molecules.
>>> 
>>> -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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> -- 
> ==
> 
> 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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <http://mackerell.umaryland.edu/~jalemkul>
> 
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Re: [gmx-users] Replica Exchange for surface tension

[gozde ergin]

I use Charmm36 force field. Do you mean the force field parameter between 
cocobetaine and SDS? Because for pure surfactant I am able to estimate the 
correct surface tension. Which means force field parameter of SDS-water and 
cocobetaine-water is fine.

Sent from my iPhone

> On 28 Mar 2017, at 7:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
>> On 3/28/17 12:43 PM, gozde ergin wrote:
>> I have a mixed system of SDS and cocobetaine on water surface.
>> I estimated the surface tension of SDS on water surface and cocabetaine on 
>> surface tension separately and correctly (comparing with experimental 
>> results).
>> However I could not estimate the correct surface tension for SDS-cocobetaine 
>> mix in even 150 ns simulation.
>> Do you think replica exchange simulation would help me to estimate the 
>> correct surface tension of mixed system?
>> Do you have any idea why I failed in estimating the mixed system surface 
>> tension?
>> 
> 
> If a physical model fails to produce known physical properties, the problem 
> is often the model itself.  I'd suspect the force field parameters first.  
> What is the source of your parameters?
> 
> Replica exchange helps you get over large barriers to improve sampling, but I 
> doubt that's useful here in a mixture of small molecules.
> 
> -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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[gmx-users] Replica Exchange for surface tension

[gozde ergin]

I have a mixed system of SDS and cocobetaine on water surface.
I estimated the surface tension of SDS on water surface and cocabetaine on 
surface tension separately and correctly (comparing with experimental results).
However I could not estimate the correct surface tension for SDS-cocobetaine 
mix in even 150 ns simulation.
Do you think replica exchange simulation would help me to estimate the correct 
surface tension of mixed system?
Do you have any idea why I failed in estimating the mixed system surface 
tension?

Thanks in advance.

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[gmx-users] mindist in gromacs

[gozde ergin]

Dear all,

I am trying to calculate the minimum distance between head groups on the water 
surface.
I used the gmx mindist tool in Gromacs however I am not sure what is the 
meaning of this distance?
Is it the distance according to x or y or z axis? 
Or is there a way to estimate the minimum distance in z,x and y axis separately?

Thanks in advance.


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Re: [gmx-users] Potential energy in Zwanzig relationship

[gozde ergin]

Dear Michael.

Thanks for the reply. I have already used this python code however I would like 
to calculate myself by using the potential energies.
Because I need to reweigh the free energy by using exponential re-weighting 
technique.
> On 10 Feb 2017, at 14:44, Michael Shirts <mrshi...@gmail.com> wrote:
> 
> https://github.com/MobleyLab/alchemical-analysis
> 
> Takes gromacs dhdl.xvg output and calculate free energies by many different
> methods, including BAR, MBAR and Zwanzig.  See
> http://www.alchemistry.org/wiki/Main_Page for more information.
> 
> On Fri, Feb 10, 2017 at 5:26 AM, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
>> Dear all,
>> 
>> I run thermodynamic integration simulation with gromacs and got the free
>> energy by g_bar command.
>> I also would like to estimate this free energy by using Zwanzig
>> relationship of \DeltaG = -RT ln (<exp{-\Delta U_(ij)/RT}>_i
>> Here U is the potential energy, right?
>> However the results that I am getting with g_bar (82 kcal/mol) and with
>> Zwanzig equation (406 kcal/mol) are totally different.
>> Do anyone has an idea why I am getting that different results?
>> 
>> Bests
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[gmx-users] Potential energy in Zwanzig relationship

[gozde ergin]

Dear all,

I run thermodynamic integration simulation with gromacs and got the free energy 
by g_bar command.
I also would like to estimate this free energy by using Zwanzig relationship of 
\DeltaG = -RT ln (_i 
Here U is the potential energy, right? 
However the results that I am getting with g_bar (82 kcal/mol) and with Zwanzig 
equation (406 kcal/mol) are totally different. 
Do anyone has an idea why I am getting that different results?

Bests
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Re: [gmx-users] g_wham PMF Profiles

[gozde ergin]

Hi Zeynep,

As you exclude the window, you lost the local information. But even excluded 
PMF profile does not seem that ’smooth’.
What is your simulation time? And maybe you may think of pulling slower like 
0.01 nm spacing.

bests (iyi calismalar)
> On 10 Feb 2017, at 08:57, ZEYNEP ABALI  wrote:
> 
> https://drive.google.com/open?id=0B4ZoiZnocOaQdGpQMkpDX0V6c1E 
> 
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Re: [gmx-users] Segmentation fault in MDRUN

[gozde ergin]

You may try with dt = 0.001. Also maybe you can increase the equilibration 
time. 



On 25 Jan 2017, at 09:30, Matteo Busato  wrote:
> 
> dt   = 0.002

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Re: [gmx-users] G_ENERGY COMMAND

[gozde ergin]

gmx energy should be the correct command.
> On 13 Jan 2017, at 10:53, Subashini .K  wrote:
> 
> 
> Hi gromacs users,
> 
> 
> I am using gromacs in windows 7, 64 bit.
> 
> 
> When the following command was given,
> 
> 
> gmx g_energy -f ener.part0001.edr -o vol.xvg
> 
> 
> 
> the error was
> 
> 
> GROMACS:  gmx, VERSION 5.1.1
> Executable:   /usr/local/gromacs/bin/gmx.exe
> Data prefix:  /usr/local/gromacs
> Command line:
>  gmx g_energy -f ener.part0001.edr -o vol.xvg
> 
> ---
> Program: gmx, VERSION 5.1.1
> Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 376)
> Function:gmx::CommandLineModuleInterface* 
> gmx::CommandLineModuleManager::Impl::processCommonOptions(gmx::CommandLineCommonOptionsHolder*,
>  int*, char***)
> 
> Error in user input:
> 'g_energy' is not a GROMACS command.
> 
> How to fix it? What is the correct command?
> 
> 
> Thanks,
> Subashini.K
> 
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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

The x-axis of the first figures on the link represents the lambda values for 
coulombic and van der waals decoupling. First ten values are for Coulombic 
interactions, last 20 values are for van der waals. So basically I thought to 
see a minima in this figure at lambda between 18-24 (which is 0.6-0.8 in 
vow-lambda values). Do you have any idea why I could not see any minima or 
should I see a minima?

Thanks in advance.
> On 13 Nov 2016, at 13:19, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Hi all,
> 
> I tried to estimate the free energy of betaine on betaine covered surface. My 
> target molecule is also on the surface.
> In order to do that I turn off charges linearly, then turn off LJ with a 
> sort-core potential. 
> Lambda is increased with 0.1 intervals for coulombic part and 0.05 intervals 
> for LJ.
> I did NVT simulation and I applied a flat-bottom potential on surface 
> molecules.
> However the result seems a little bit strange, first I could not see any 
> minima in free energy from lambda 0 to 1 (I assume there should be minima 
> aroma lambda=0.6-0.7). 
> Also my histogram plot also seems strange that I have very big numbers on x 
> axis (like e+33).
> Please see the plots link below.
> 
> https://imgur.com/a/fqgmi
> 
> Any help would be appreciated.
> Thanks.
>> On 06 Nov 2016, at 14:33, Justin Lemkul <jalem...@vt.edu> wrote:
>> 
>> 
>> 
>> On 11/6/16 8:27 AM, gozde ergin wrote:
>>> 
>>>> If it's the salt, then take the known Na+ value for the force field and 
>>>> add it to the SDS value you obtain at infinite dilution. Straightforward.
>>> 
>>> Ok either I can take hydration free energy of Na from the literature or I 
>>> can run 2 thermodynamic integration with dodecyl sulfate and Na separately 
>>> and sum them.
>>> 
>> 
>> Yes, because DeltaG is a state function.
>> 
>>> Besides this I would like ask how did you manage the get the very similar 
>>> solvation free energy result with experiments without adding Coulomb 
>>> interaction which means decoupling only the L-J?
>> 
>> The reference quantity is just the LJ component of the total free energy; 
>> please see the referenced paper by Shirts et al.  Methane is net-neutral and 
>> the LJ will dominate, anyway, but the quantity shown (and explicitly stated) 
>> is NOT the hydration free energy, just part of it.
>> 
>>> Do you think to estimate the correct solvation free energy for dodecyl 
>>> sufate(-) and Na(+) I need to decouple also the Coulombic interaction?
>> 
>> Of course, those will be critical for charged species.
>> 
>>> If yes, in order to do that I just need to modify the coul_lambdas 
>>> parameter in .mdp file, right?
>> 
>> Yes.
>> 
>>> Also I should not make the charge of the atoms as zero in topology file.
>> 
>> Correct.
>> 
>>> According to the Sander Pronk tutorial of Solvation free energy of ethanol, 
>>> I can turn off both the electrostatic (Coulomb) interactions and the Van 
>>> der Waals (Lennard-Jones) interactions at the same time.
>>> 
>> 
>> This may be unstable, and is generally not done.  Turn off charges linearly, 
>> then turn off LJ with a soft-core potential (or vice versa).  The point is 
>> you should never have charges on atoms with no (or drastically reduced) LJ 
>> terms. This can be easily specified in an appropriate series of lambda 
>> states in the .mdp file.
>> 
>> -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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>> mail to gmx-users-requ...@gromacs.org.
> 

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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Hi all,

I tried to estimate the free energy of betaine on betaine covered surface. My 
target molecule is also on the surface.
In order to do that I turn off charges linearly, then turn off LJ with a 
sort-core potential. 
Lambda is increased with 0.1 intervals for coulombic part and 0.05 intervals 
for LJ.
I did NVT simulation and I applied a flat-bottom potential on surface molecules.
However the result seems a little bit strange, first I could not see any minima 
in free energy from lambda 0 to 1 (I assume there should be minima aroma 
lambda=0.6-0.7). 
Also my histogram plot also seems strange that I have very big numbers on x 
axis (like e+33).
Please see the plots link below.

https://imgur.com/a/fqgmi

Any help would be appreciated.
Thanks.
> On 06 Nov 2016, at 14:33, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 11/6/16 8:27 AM, gozde ergin wrote:
>> 
>>> If it's the salt, then take the known Na+ value for the force field and add 
>>> it to the SDS value you obtain at infinite dilution. Straightforward.
>> 
>> Ok either I can take hydration free energy of Na from the literature or I 
>> can run 2 thermodynamic integration with dodecyl sulfate and Na separately 
>> and sum them.
>> 
> 
> Yes, because DeltaG is a state function.
> 
>> Besides this I would like ask how did you manage the get the very similar 
>> solvation free energy result with experiments without adding Coulomb 
>> interaction which means decoupling only the L-J?
> 
> The reference quantity is just the LJ component of the total free energy; 
> please see the referenced paper by Shirts et al.  Methane is net-neutral and 
> the LJ will dominate, anyway, but the quantity shown (and explicitly stated) 
> is NOT the hydration free energy, just part of it.
> 
>> Do you think to estimate the correct solvation free energy for dodecyl 
>> sufate(-) and Na(+) I need to decouple also the Coulombic interaction?
> 
> Of course, those will be critical for charged species.
> 
>> If yes, in order to do that I just need to modify the coul_lambdas parameter 
>> in .mdp file, right?
> 
> Yes.
> 
>> Also I should not make the charge of the atoms as zero in topology file.
> 
> Correct.
> 
>> According to the Sander Pronk tutorial of Solvation free energy of ethanol, 
>> I can turn off both the electrostatic (Coulomb) interactions and the Van der 
>> Waals (Lennard-Jones) interactions at the same time.
>> 
> 
> This may be unstable, and is generally not done.  Turn off charges linearly, 
> then turn off LJ with a soft-core potential (or vice versa).  The point is 
> you should never have charges on atoms with no (or drastically reduced) LJ 
> terms. This can be easily specified in an appropriate series of lambda states 
> in the .mdp file.
> 
> -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] Umbrella Sampling

[gozde ergin]

Hey,

Did you change the number inside the distances.pl script?
If you have 1000 files, you need to change the number of 500 on line 6, 13 , 
and  36 (lines start with for loop) make them 1000.
> On 13 Nov 2016, at 11:10, Mouri Ahmed  wrote:
> 
> Hi everyone,
> 
> I have run pulling simulation for the protein complex system. I have got
> 1000 configuration files. And in the summary_distances.dat, I have found
> 0-500 distances.
> 
> How will I select configuration file for the npt_umbrella simulation.
> 
> Thanks in advance. I will be very grateful for the help.
> 
> Best Regards
> Mouri
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[gmx-users] MBAR issue

[gozde ergin]

Dear all,

I follow James Barnett tutorial of “Methane Free Energy of Solvation” however I 
use betaine molecule other than methane.
In order to analyse the data I use alchemical_analysis.py code however I get an 
error :

pymbar.utils.ParameterError: Warning: Should have \sum_k N_k W_nk = 1.  Actual 
row sum for sample 0 was 1.307134. 663638 other rows have similar problems

Do you have any idea about the error or anyone here face with this error?
Thanks in advance.
Bests regards.
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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Thanks a lot Justin,
Everything is more clear right now.
Bests

> On 06 Nov 2016, at 17:30, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 11/6/16 10:44 AM, gozde ergin wrote:
>> 
>>> This may be unstable, and is generally not done.  Turn off charges
>>> linearly, then turn off LJ with a soft-core potential (or vice versa).  The
>>> point is you should never have charges on atoms with no (or drastically
>>> reduced) LJ terms. This can be easily specified in an appropriate series of
>>> lambda states in the .mdp file.
>> 
>> So basically atomic partial charges should be reduced to zero by
>> thermodynamic integration (TI) ,than van der Waals interactions should be
>> removed from the now chargeless module in a TI calculation using a soft-core
>> LJ potential (as in you tutorial). On the other hand I do not need to use
>> soft-core in on the fist coulombic interaction calculation, right?
>> 
> 
> TI (like BAR, FEP, WHAM, etc) is a method of analysis for evaluating free 
> energy differences.  There is no TI during the calculation.  It's a 
> lambda-dependent scaling of the interactions, but otherwise this is correct.  
> One can choose to use a soft-core potential for the electrostatics, but I've 
> never found a need for it.
> 
> -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] Questions about free energy calculation tutorial

[gozde ergin]

> This may be unstable, and is generally not done.  Turn off charges linearly, 
> then turn off LJ with a soft-core potential (or vice versa).  The point is 
> you should never have charges on atoms with no (or drastically reduced) LJ 
> terms. This can be easily specified in an appropriate series of lambda states 
> in the .mdp file.

So basically atomic partial charges should be reduced to zero by thermodynamic 
integration (TI) ,than van der Waals interactions should be removed from the 
now chargeless module in a TI calculation using a soft-core LJ potential (as in 
you tutorial). On the other hand I do not need to use soft-core in on the fist 
coulombic interaction calculation, right?

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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

> If it's the salt, then take the known Na+ value for the force field and add 
> it to the SDS value you obtain at infinite dilution. Straightforward.

Ok either I can take hydration free energy of Na from the literature or I can 
run 2 thermodynamic integration with dodecyl sulfate and Na separately and sum 
them.

Besides this I would like ask how did you manage the get the very similar 
solvation free energy result with experiments without adding Coulomb 
interaction which means decoupling only the L-J?
Do you think to estimate the correct solvation free energy for dodecyl 
sufate(-) and Na(+) I need to decouple also the Coulombic interaction?
If yes, in order to do that I just need to modify the coul_lambdas parameter in 
.mdp file, right?
Also I should not make the charge of the atoms as zero in topology file. 
According to the Sander Pronk tutorial of Solvation free energy of ethanol, I 
can turn off both the electrostatic (Coulomb) interactions and the Van der 
Waals (Lennard-Jones) interactions at the same time.
 

 



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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

> If you need the total free energy of hydration for NaSDS, you can just 
> decouple SDS in water with no Na+ and sum the two contributions (SDS and Na+ 
> separately).  If you just want the SDS hydration free energy, decouple it in 
> a box of pure water

Thanks Justin, 

I have difficulty to understand NaSDS? SDS is Sodium dodecyl sulfate so Na is 
in this molecule.

What about running the simulation with both Na ions and dodecyl sulfate inside 
the water. However I just decouple the dodecyl sulfate part. 
I also make the charge of Na ions zero so I can run the simulation with net 0 
(zero) charge. 
Na ions will physically be there but their charge will be zero. 
Is not this more closer to experimental SDS hydration state? 

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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Thank Justin, ok I understand now. 
Then I need to run the simulation with +1 charge, since I made 0 of all the 
charges in SDS, Na+ charge will stay there.
Do you think it is ok run with +1 charge?

> On 04 Nov 2016, at 13:36, Justin Lemkul  wrote:
> 
> No, you should not.  The topology you posted before had Na+ as part of the 
> SDS [moleculetype] and you were decoupling the whole thing.  This is what I 
> am saying you should not be doing if you're trying to get just the hydration 
> free energy of SDS.
> 
> -Justin

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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

> If you want the hydration free energy of SDS, you should not include Na+ 
> because the simultaneous decoupling will include the hydration free energy of 
> Na+.  You can subtract that out, but there is error associated with that 
> calculation and accounting for that is not necessarily easy.  It is 
> straightforward to just deal with SDS alone.

Yes this is exactly what I want but I did not get how the Na+ would be included 
simultaneously? 
My SDS.itp file contains C12H25SO4- molecules, Na+ is not inside this file. 
There is another SOD.itp file that contains Na+. 
So if I only write SDS to couple-moltype in .mdp file, it will decouple 
C12H25SO4- but not Na+. 
Should I put Na+ atom inside the SDS.itp?

> On 04 Nov 2016, at 12:51, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 11/3/16 10:56 AM, gozde ergin wrote:
>>> You can decouple atomic and molecular ions, there are just additional 
>>> considerations like an interface potential to calculate.  See, e.g. work by 
>>> Benoit Roux.
>> 
>> Yes I can but do I need to? I just want to know the free energy of solvation 
>> of SDS. If I do not include the Na ion decoupling, is it wrong?
>> 
> 
> I
> 
> -Justin
> 
>>> On 02 Nov 2016, at 12:42, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 11/1/16 9:02 AM, gozde ergin wrote:
>>>>>> This is a generic simulation failure message, indicating that your 
>>>>>> system is blowing up.  This could be due to any number of reasons, but 
>>>>>> without more details it's pointless to guess.
>>>> 
>>>> If I do not include the Na ion in decoupling I do not have this warning.
>>>> If I do not decouple Na ion still I need to make the charge of this 
>>>> molecule zero otherwise system charge becomes +1.
>>>> 
>>>>>> Decoupling the Na+ ion will mean your resulting dG value includes the 
>>>>>> hydration free energy of Na+, which it doesn't sound like you're 
>>>>>> interested in.
>>>> 
>>>> My purpose is doing the same thing with SDS that you did with Methane. And 
>>>> as SDS has Na ion I thought I need also to decouple it.
>>>> Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
>>>> Last question even if I do not decouple the Na ion I need to make it 
>>>> charge zero, right?
>>>> 
>>> 
>>> You can decouple atomic and molecular ions, there are just additional 
>>> considerations like an interface potential to calculate.  See, e.g. work by 
>>> Benoit Roux.
>>> 
>>> -Justin
>>> 
>>>> Thanks in advance.
>>>>> On 01 Nov 2016, at 13:21, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>> 
>>>>> 
>>>>> 
>>>>> On 11/1/16 7:31 AM, gozde ergin wrote:
>>>>>> Hi Justin,
>>>>>> 
>>>>>> I would like to ask one question related to this tutorial. I do the same 
>>>>>> thing with using SDS (Sodium dodecyl sulfate) molecule.
>>>>>> As you know there is NA (Sodium) atom that not bonded to dodecyl 
>>>>>> sulphate part. However in order to estimate the free energy of SDS 
>>>>>> salvation in water I need to decouple the all SDS molecule. Since 
>>>>>> couple-moltype accept only one types of molecule, I hacked the topology 
>>>>>> and put all atoms I want to decouple in the same [moleculetype] :
>>>>>> 
>>>>>> [ moleculetype ]
>>>>>> ; name   nrexcl
>>>>>> SDS   3
>>>>>> 
>>>>>> [ atoms ]
>>>>>> ; nr typeresnr   residu  atomcgnrcharge  mass
>>>>>>   1 SL  1  SDS  S  1  0.00032.0600   ; 
>>>>>> qtot  1.330
>>>>>>   2OSL  1  SDSOS1  2  0.00015.9994   ; 
>>>>>> qtot  1.050
>>>>>>   3O2L  1  SDSOS2  3  0.00015.9994   ; 
>>>>>> qtot  0.400
>>>>>>   4O2L  1  SDSOS3  4  0.00015.9994   ; 
>>>>>> qtot -0.250
>>>>>>   5O2L  1  SDSOS4  5  0.00015.9994   ; 
>>>>>> qtot -0.900
>>>>>>.
>>>>>>.
>>>>>>  25   HAL2  1  SDSH71 25  0.000 

Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

> You can decouple atomic and molecular ions, there are just additional 
> considerations like an interface potential to calculate.  See, e.g. work by 
> Benoit Roux.

Yes I can but do I need to? I just want to know the free energy of solvation of 
SDS. If I do not include the Na ion decoupling, is it wrong?

> On 02 Nov 2016, at 12:42, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 11/1/16 9:02 AM, gozde ergin wrote:
>>>> This is a generic simulation failure message, indicating that your system 
>>>> is blowing up.  This could be due to any number of reasons, but without 
>>>> more details it's pointless to guess.
>> 
>> If I do not include the Na ion in decoupling I do not have this warning.
>> If I do not decouple Na ion still I need to make the charge of this molecule 
>> zero otherwise system charge becomes +1.
>> 
>>>> Decoupling the Na+ ion will mean your resulting dG value includes the 
>>>> hydration free energy of Na+, which it doesn't sound like you're 
>>>> interested in.
>> 
>> My purpose is doing the same thing with SDS that you did with Methane. And 
>> as SDS has Na ion I thought I need also to decouple it.
>> Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
>> Last question even if I do not decouple the Na ion I need to make it charge 
>> zero, right?
>> 
> 
> You can decouple atomic and molecular ions, there are just additional 
> considerations like an interface potential to calculate.  See, e.g. work by 
> Benoit Roux.
> 
> -Justin
> 
>> Thanks in advance.
>>> On 01 Nov 2016, at 13:21, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 11/1/16 7:31 AM, gozde ergin wrote:
>>>> Hi Justin,
>>>> 
>>>> I would like to ask one question related to this tutorial. I do the same 
>>>> thing with using SDS (Sodium dodecyl sulfate) molecule.
>>>> As you know there is NA (Sodium) atom that not bonded to dodecyl sulphate 
>>>> part. However in order to estimate the free energy of SDS salvation in 
>>>> water I need to decouple the all SDS molecule. Since couple-moltype accept 
>>>> only one types of molecule, I hacked the topology and put all atoms I want 
>>>> to decouple in the same [moleculetype] :
>>>> 
>>>> [ moleculetype ]
>>>> ; name nrexcl
>>>> SDS 3
>>>> 
>>>> [ atoms ]
>>>> ; nr   typeresnr   residu  atomcgnrcharge  mass
>>>>1 SL  1  SDS  S  1  0.00032.0600   ; 
>>>> qtot  1.330
>>>>2OSL  1  SDSOS1  2  0.00015.9994   ; 
>>>> qtot  1.050
>>>>3O2L  1  SDSOS2  3  0.00015.9994   ; 
>>>> qtot  0.400
>>>>4O2L  1  SDSOS3  4  0.00015.9994   ; 
>>>> qtot -0.250
>>>>5O2L  1  SDSOS4  5  0.00015.9994   ; 
>>>> qtot -0.900
>>>> .
>>>> .
>>>>   25   HAL2  1  SDSH71 25  0.000 1.0080   ; 
>>>> qtot -1.090
>>>>   26   HAL2  1  SDSH72 26  0.000 1.0080   ; 
>>>> qtot -1.000
>>>>   27   CTL2  1  SDS C8 27  0.00012.0110   ; 
>>>> qtot -1.180
>>>>.
>>>>.
>>>>   42   HAL3  1  SDS   H123 42  0.000 1.0080   ; 
>>>> qtot -1.000
>>>>   43SOD  2  SDSSOD 43  0.00022.9898   ; 
>>>> qtot  1.000
>>>> .
>>>> 
>>>> However I get this warning during the simulation :
>>>> 
>>>> WARNING: Listed nonbonded interaction between particles 25 and 43
>>>> at distance 2.303 which is larger than the table limit 2.200 nm.
>>>> 
>>>> Do you have any idea how could I get rid off this warning?
>>>> 
>>> 
>>> This is a generic simulation failure message, indicating that your system 
>>> is blowing up.  This could be due to any number of reasons, but without 
>>> more details it's pointless to guess.
>>> 
>>>> Also does the hacked .top file seem correct?
>>>> 
>>> 
>>> Decoupling the Na+ ion will mean your resulting dG value includes the 
>>> hydration free energy of Na+, which it doesn't sound like you're inte

Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

>>This is a generic simulation failure message, indicating that your system is 
>>blowing up.  This could be due to any number of reasons, but without more 
>>details it's pointless to guess.

If I do not include the Na ion in decoupling I do not have this warning. 
If I do not decouple Na ion still I need to make the charge of this molecule 
zero otherwise system charge becomes +1.

>>Decoupling the Na+ ion will mean your resulting dG value includes the 
>>hydration free energy of Na+, which it doesn't sound like you're interested 
>>in.

My purpose is doing the same thing with SDS that you did with Methane. And as 
SDS has Na ion I thought I need also to decouple it.
Do you think I do not need to decouple the Na ion but only dodecyl sulfate?
Last question even if I do not decouple the Na ion I need to make it charge 
zero, right?

Thanks in advance.
> On 01 Nov 2016, at 13:21, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 11/1/16 7:31 AM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I would like to ask one question related to this tutorial. I do the same 
>> thing with using SDS (Sodium dodecyl sulfate) molecule.
>> As you know there is NA (Sodium) atom that not bonded to dodecyl sulphate 
>> part. However in order to estimate the free energy of SDS salvation in water 
>> I need to decouple the all SDS molecule. Since couple-moltype accept only 
>> one types of molecule, I hacked the topology and put all atoms I want to 
>> decouple in the same [moleculetype] :
>> 
>> [ moleculetype ]
>> ; name   nrexcl
>> SDS   3
>> 
>> [ atoms ]
>> ; nr typeresnr   residu  atomcgnrcharge  mass
>> 1 SL  1  SDS  S  1  0.00032.0600   ; 
>> qtot  1.330
>> 2OSL  1  SDSOS1  2  0.00015.9994   ; 
>> qtot  1.050
>> 3O2L  1  SDSOS2  3  0.00015.9994   ; 
>> qtot  0.400
>> 4O2L  1  SDSOS3  4  0.00015.9994   ; 
>> qtot -0.250
>> 5O2L  1  SDSOS4  5  0.00015.9994   ; 
>> qtot -0.900
>>  .
>>  .
>>25   HAL2  1  SDSH71 25  0.000 1.0080   ; 
>> qtot -1.090
>>26   HAL2  1  SDSH72 26  0.000 1.0080   ; 
>> qtot -1.000
>>27   CTL2  1  SDS C8 27  0.00012.0110   ; 
>> qtot -1.180
>> .
>> .
>>42   HAL3  1  SDS   H123 42  0.000 1.0080   ; 
>> qtot -1.000
>>43SOD  2  SDSSOD 43  0.00022.9898   ; 
>> qtot  1.000
>> .
>> 
>> However I get this warning during the simulation :
>> 
>> WARNING: Listed nonbonded interaction between particles 25 and 43
>> at distance 2.303 which is larger than the table limit 2.200 nm.
>> 
>> Do you have any idea how could I get rid off this warning?
>> 
> 
> This is a generic simulation failure message, indicating that your system is 
> blowing up.  This could be due to any number of reasons, but without more 
> details it's pointless to guess.
> 
>> Also does the hacked .top file seem correct?
>> 
> 
> Decoupling the Na+ ion will mean your resulting dG value includes the 
> hydration free energy of Na+, which it doesn't sound like you're interested 
> in.
> 
> -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
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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Hi Justin,

I would like to ask one question related to this tutorial. I do the same thing 
with using SDS (Sodium dodecyl sulfate) molecule.
As you know there is NA (Sodium) atom that not bonded to dodecyl sulphate part. 
However in order to estimate the free energy of SDS salvation in water I need 
to decouple the all SDS molecule. Since couple-moltype accept only one types of 
molecule, I hacked the topology and put all atoms I want to decouple in the 
same [moleculetype] :

[ moleculetype ]
; name  nrexcl
SDS  3

[ atoms ]
; nrtyperesnr   residu  atomcgnrcharge  mass
 1 SL  1  SDS  S  1  0.00032.0600   ; qtot  
1.330
 2OSL  1  SDSOS1  2  0.00015.9994   ; qtot  
1.050
 3O2L  1  SDSOS2  3  0.00015.9994   ; qtot  
0.400
 4O2L  1  SDSOS3  4  0.00015.9994   ; qtot 
-0.250
 5O2L  1  SDSOS4  5  0.00015.9994   ; qtot 
-0.900
  . 
  .
25   HAL2  1  SDSH71 25  0.000 1.0080   ; qtot 
-1.090
26   HAL2  1  SDSH72 26  0.000 1.0080   ; qtot 
-1.000
27   CTL2  1  SDS C8 27  0.00012.0110   ; qtot 
-1.180
 .
 .
42   HAL3  1  SDS   H123 42  0.000 1.0080   ; qtot 
-1.000
43SOD  2  SDSSOD 43  0.00022.9898   ; qtot  
1.000
.

However I get this warning during the simulation : 

WARNING: Listed nonbonded interaction between particles 25 and 43
at distance 2.303 which is larger than the table limit 2.200 nm.

Do you have any idea how could I get rid off this warning?

Also does the hacked .top file seem correct?

Thanks a lot!






> On 28 Oct 2016, at 17:05, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 10/28/16 4:22 AM, gozde ergin wrote:
>> Thanks Justin,
>> 
>> Actually for my case I’ll put the methane molecule inside cubic box not 
>> spherical.
> 
> The geometry of the restraint is what is relevant.  If it's a spherical 
> flat-bottom potential (the easiest thing to use) then you need to account for 
> a spherical restriction.  The cube is periodic, so its shape is irrelevant.
> 
>> There is method called  'Boltzmann exponential reweighting’, however I could 
>> not figure out how to apply this method to methane-water system.
>> With the command of g_energy I could get the flat-bottom restraint energy, 
>> do you think I just need to remove these energy from the result \DeltaG?
>> I would like to learn if you have any idea and source to suggest.
> 
> It's not just something g_energy can subtract out; you're changing the 
> entropy by a factor related to the volume.  It should be something like 
> -RTln(V/V0) where V0 is the molar volume in the gas phase and V is the volume 
> to which you are restricting the molecule.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 27 Oct 2016, at 20:58, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 10/27/16 11:35 AM, gozde ergin wrote:
>>>> Dear all,
>>>> 
>>>> I follow the Justin’s free energy calculations: Methane in Water tutorial. 
>>>> (Thanks Justin!)
>>>> I would like to ask two questions:
>>>> 
>>>> 1) Is there specific reason to use sd integrator?
>>> 
>>> Langevin dynamics gives better sampling.
>>> 
>>>> 2) Methane molecules is free to sample every x,y,z point in the water bulk.
>>>>   I would like to apply a flat-bottom restraint and keep methane molecule 
>>>> in the centre of bulk.
>>>>   I want to prevent methane movement in z direction.
>>>>   Do you have any idea how to remove the effect of flat-bottom restraint 
>>>> afterwards?
>>>> 
>>> 
>>> You're confining it to a spherical volume, so you need to account for that 
>>> entropic contribution.
>>> 
>>> -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
>>> 
>>> ==
>>> --
>>> G

Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Ok thanks Justin!
> On 28 Oct 2016, at 17:05, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 10/28/16 4:22 AM, gozde ergin wrote:
>> Thanks Justin,
>> 
>> Actually for my case I’ll put the methane molecule inside cubic box not 
>> spherical.
> 
> The geometry of the restraint is what is relevant.  If it's a spherical 
> flat-bottom potential (the easiest thing to use) then you need to account for 
> a spherical restriction.  The cube is periodic, so its shape is irrelevant.
> 
>> There is method called  'Boltzmann exponential reweighting’, however I could 
>> not figure out how to apply this method to methane-water system.
>> With the command of g_energy I could get the flat-bottom restraint energy, 
>> do you think I just need to remove these energy from the result \DeltaG?
>> I would like to learn if you have any idea and source to suggest.
> 
> It's not just something g_energy can subtract out; you're changing the 
> entropy by a factor related to the volume.  It should be something like 
> -RTln(V/V0) where V0 is the molar volume in the gas phase and V is the volume 
> to which you are restricting the molecule.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 27 Oct 2016, at 20:58, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 10/27/16 11:35 AM, gozde ergin wrote:
>>>> Dear all,
>>>> 
>>>> I follow the Justin’s free energy calculations: Methane in Water tutorial. 
>>>> (Thanks Justin!)
>>>> I would like to ask two questions:
>>>> 
>>>> 1) Is there specific reason to use sd integrator?
>>> 
>>> Langevin dynamics gives better sampling.
>>> 
>>>> 2) Methane molecules is free to sample every x,y,z point in the water bulk.
>>>>   I would like to apply a flat-bottom restraint and keep methane molecule 
>>>> in the centre of bulk.
>>>>   I want to prevent methane movement in z direction.
>>>>   Do you have any idea how to remove the effect of flat-bottom restraint 
>>>> afterwards?
>>>> 
>>> 
>>> You're confining it to a spherical volume, so you need to account for that 
>>> entropic contribution.
>>> 
>>> -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
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>>> 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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==
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Re: [gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Thanks Justin,

Actually for my case I’ll put the methane molecule inside cubic box not 
spherical. 
There is method called  'Boltzmann exponential reweighting’, however I could 
not figure out how to apply this method to methane-water system.
With the command of g_energy I could get the flat-bottom restraint energy, do 
you think I just need to remove these energy from the result \DeltaG?
I would like to learn if you have any idea and source to suggest.
Thanks in advance.


> On 27 Oct 2016, at 20:58, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 10/27/16 11:35 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I follow the Justin’s free energy calculations: Methane in Water tutorial. 
>> (Thanks Justin!)
>> I would like to ask two questions:
>> 
>> 1) Is there specific reason to use sd integrator?
> 
> Langevin dynamics gives better sampling.
> 
>> 2) Methane molecules is free to sample every x,y,z point in the water bulk.
>>I would like to apply a flat-bottom restraint and keep methane molecule 
>> in the centre of bulk.
>>I want to prevent methane movement in z direction.
>>Do you have any idea how to remove the effect of flat-bottom restraint 
>> afterwards?
>> 
> 
> You're confining it to a spherical volume, so you need to account for that 
> entropic contribution.
> 
> -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] Questions about free energy calculation tutorial

[gozde ergin]

Dear all,

I follow the Justin’s free energy calculations: Methane in Water tutorial. 
(Thanks Justin!)
I would like to ask two questions:

1) Is there specific reason to use sd integrator? 
2) Methane molecules is free to sample every x,y,z point in the water bulk. 
I would like to apply a flat-bottom restraint and keep methane molecule in 
the centre of bulk.
I want to prevent methane movement in z direction. 
Do you have any idea how to remove the effect of flat-bottom restraint 
afterwards? 

Thanks in advance.
Bests

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[gmx-users] Partial charges correction from PRODRG

[gozde ergin]

Dear all,

Thanks to the Lemkul et.al. 2010 paper, we know that charges are often 
inconsistent in topologies produced by PRODRG.
I have two types organic molecules to simulate, SDS and C12betaine.
There are a lot of studies about SDS so I found the optimised charge 
distribution for Gromos-UA force field for SDS.
However I struggle to optimise the C12betaine charges.
Do you have any hint to optimise the C12betaine charges for Gromos-UA?

Any help would be appreciated.
Thanks in advance.

Bests
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Re: [gmx-users] Umbrella sampling tutorial

[gozde ergin]

Any idea on this topic?

Thanks
> On 07 Oct 2016, at 14:13, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Thanks Justin.
> I want infinite dilute bulk that’s why I do not want any surfactant molecule 
> inside the bulk.
> I may put a ‘’wall’’ just below the surface molecules in order to inhibit 
> their travel to bulk but I do not know how to remove this effect from PMF.
> 
> 
>> On 07 Oct 2016, at 13:40, Justin Lemkul <jalem...@vt.edu> wrote:
>> 
>> 
>> 
>> On 10/7/16 4:41 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I would like to ask a question about Justin’s tutorial. By using the
>>> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
>>> effect of this restraint removed during the WHAM?
>>> 
>> 
>> Not to my knowledge, no.  The restraints in the tutorial are there to mimic 
>> the fact that there are only five peptides, when in reality, there are 
>> millions, so the effects of the forces are quite different in vitro/in vivo. 
>>  Restraining one peptide makes the remaining four peptides more stable, more 
>> realistic.  WHAM doesn't do anything to change this.
>> 
>>> I want to do a similar thing by applying restraint force on the organic
>>> molecule on the bulk water in order to inhibit their movement inside the
>>> bulk. Should I consider the removing of the restraint in PMF?
>>> 
>> 
>> In the case of freely diffusing molecules, I suspect such a restraint would 
>> have a much more profound impact.  Why do you want to do this?
>> 
>> -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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> 

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[gmx-users] Re-center the trajectory

[gozde ergin]

Dear all,

After 20 ns simulation I would like to re-center my trajectory according to the 
"centre of box” which is 2.4 2.4 15.
I almost tried all trjconv options (-pbc with mol, -center, -ur compact) 
however the trajectory still moves the +z/-z direction.
Is there any way to re-center the molecules according to the center of box?

Thanks
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Re: [gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Hi Alex,

I thought by getting the flat-bottom restraint potential on my target molecule 
I should be able to get the free energy of unbiased case.
Basically; P(q)=P’(q)exp(V(q)/kBT) Here P is unbiased probability, P’ is biased 
probability and V is added potential.
However I am not totally sure. 

You can check http://plumed.github.io/doc-v2.2/user-doc/html/belfast-4.html 
<http://plumed.github.io/doc-v2.2/user-doc/html/belfast-4.html>


On 17 Oct 2016, at 18:56, Alex <alexanderwie...@gmail.com> wrote:
> 
> Hi Gozde,
> 
> I also use something similar, by an simple pull restrain(distance) to keep
> a counter ion close to the charged molecule which is under perturbation in
> FEP.
> These type of restrains are \*Lambda  *independent and if I am not wrong
> their portion in free energy change should be calculated analytically by a
> formula like something you will see in below link in its "removal of
> restrains" section;
> 
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
> 
> But I have not been able to use it applicably, and I would be also
> appreciated if you could let me also know how to use if you find out either
> by this or ... .
> 
> Best regards,
> 
> Alex
> 
> On Mon, Oct 17, 2016 at 6:14 PM, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
>> Any idea?
>> Thanks.
>>> On 13 Oct 2016, at 15:42, gozde ergin <gozdeeer...@gmail.com> wrote:
>>> 
>>> Dear all,
>>> 
>>> I will use Gromacs to calculate the chemical potential difference of
>> solvation a surfactant molecule on the surface.
>>> System covers water molecules covered with surfactant molecules.
>>> I will apply flat-bottom restraint to the surfactant molecules in order
>> to stabilise them on surface. I will not let them to go inside the bulk.
>>> My question is how should I re-weight the free energy value to remove
>> the effect of flat-bottom restraint potential?
>>> 
>>> Thanks in advance.
>> 
>> --
>> 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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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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Re: [gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Any idea?
Thanks.
> On 13 Oct 2016, at 15:42, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Dear all,
> 
> I will use Gromacs to calculate the chemical potential difference of 
> solvation a surfactant molecule on the surface.
> System covers water molecules covered with surfactant molecules.
> I will apply flat-bottom restraint to the surfactant molecules in order to 
> stabilise them on surface. I will not let them to go inside the bulk.
> My question is how should I re-weight the free energy value to remove the 
> effect of flat-bottom restraint potential?
> 
> Thanks in advance.

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[gmx-users] Thermodynamic integration and re-weighting method

[gozde ergin]

Dear all,

I will use Gromacs to calculate the chemical potential difference of solvation 
a surfactant molecule on the surface.
System covers water molecules covered with surfactant molecules.
I will apply flat-bottom restraint to the surfactant molecules in order to 
stabilise them on surface. I will not let them to go inside the bulk.
My question is how should I re-weight the free energy value to remove the 
effect of flat-bottom restraint potential?

Thanks in advance.
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Re: [gmx-users] Umbrella sampling tutorial

[gozde ergin]

Thanks Justin.
I want infinite dilute bulk that’s why I do not want any surfactant molecule 
inside the bulk.
I may put a ‘’wall’’ just below the surface molecules in order to inhibit their 
travel to bulk but I do not know how to remove this effect from PMF.


> On 07 Oct 2016, at 13:40, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 10/7/16 4:41 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I would like to ask a question about Justin’s tutorial. By using the
>> POSRES_B, a restraint is applied on chain B in order to immobile it. Is the
>> effect of this restraint removed during the WHAM?
>> 
> 
> Not to my knowledge, no.  The restraints in the tutorial are there to mimic 
> the fact that there are only five peptides, when in reality, there are 
> millions, so the effects of the forces are quite different in vitro/in vivo.  
> Restraining one peptide makes the remaining four peptides more stable, more 
> realistic.  WHAM doesn't do anything to change this.
> 
>> I want to do a similar thing by applying restraint force on the organic
>> molecule on the bulk water in order to inhibit their movement inside the
>> bulk. Should I consider the removing of the restraint in PMF?
>> 
> 
> In the case of freely diffusing molecules, I suspect such a restraint would 
> have a much more profound impact.  Why do you want to do this?
> 
> -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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[gmx-users] Umbrella sampling tutorial

[gozde ergin]

Dear all,

I would like to ask a question about Justin’s tutorial.
By using the POSRES_B, a restraint is applied on chain B in order to immobile 
it. Is the effect of this restraint removed during the WHAM? 

I want to do a similar thing by applying restraint force on the organic 
molecule on the bulk water in order to inhibit their movement inside the bulk. 
Should I consider the removing of the restraint in PMF?

Thanks in advance.
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[gmx-users] Synergism with MD

[gozde ergin]

Dear users,

I would like ask a general question.
I want to estimate the synergism in surface tension reduction effectiveness by 
using MD.
There are experimental studies about this topic however I could not find a MD 
study.
Do you aware any MD studies related the synergism in surface tension for mixed 
surfactant?


Thanks
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Re: [gmx-users] What is the meaning of negative surface tension?

[gozde ergin]

Also when I check the pressure in X,Y and Z axis,
Pzz = -0.34 bar
Pyy = -1275 bar
Pxx = 32 bar.
Pyy and Pxx should be equal to each other. So basically system is not under 
equilibrium conditions.
How should I solve this problem? Any idea?

> On 23 Sep 2016, at 09:27, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Dear all,
> 
> I am simulating organic covered salty water system in order to estimate the 
> surface tension. Force field is Charmm36 and water model in TIP3P.
> Surface tension is -127 mN/m after 5 ns run. What is the meaning of negative 
> surface tension?
> I was expecting +30 ~ +40 mN/m but not negative. 
> Maybe my system was not under equilibrium conditions. 
> Will longer running solve the problem? Any help would be appreciated.
> 
> Thanks in advance.

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[gmx-users] What is the meaning of negative surface tension?

[gozde ergin]

Dear all,

I am simulating organic covered salty water system in order to estimate the 
surface tension. Force field is Charmm36 and water model in TIP3P.
Surface tension is -127 mN/m after 5 ns run. What is the meaning of negative 
surface tension?
I was expecting +30 ~ +40 mN/m but not negative. 
Maybe my system was not under equilibrium conditions. 
Will longer running solve the problem? Any help would be appreciated.

Thanks in advance.
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Re: [gmx-users] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Ok I will. Thank you very much Justin.
> On 02 Sep 2016, at 16:58, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 9/2/16 10:44 AM, Justin Lemkul wrote:
>> 
>> 
>> On 9/2/16 10:43 AM, gozde ergin wrote:
>>> Ok I understand. I did exactly same thing for another molecule (SDS) and
>>> everything is working without any error.
>>> But I do not know what should I do with cis-pinonic.
>>> 
>> 
>> If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I 
>> will
>> take a quick look.
>> 
> 
> Contact the CHARMM-GUI developers. The problem is that the parameters 
> specific to the cis-pinonic acid present in lig/lig.prm have not been 
> included when the force field was converted, so only parameters in the ligand 
> that are taken from the parent force field are present.  So their conversion 
> script has a bug.
> 
> -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] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Ok I understand. I did exactly same thing for another molecule (SDS) and 
everything is working without any error.
But I do not know what should I do with cis-pinonic.

> On 02 Sep 2016, at 16:40, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 9/2/16 10:39 AM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I try to use the CHARMM-GUI files directly. My purpose is simulating the 
>> water and ci-pinonic system. Cis-pionic molecules will stay on the water 
>> surface and I would like to estimate surface tension reduction.
>> 
>> What should I change in CHARMM-GUI files?
> 
> Nothing.  That's my point.  When the system is constructed, CHARMM-GUI builds 
> a PSF and list of force field parameters that it needs.  This information is 
> then converted to GROMACS format.  CHARMM-GUI does an energy evaluation to 
> confirm that everything is present.  That's why it's a bit mystifying that 
> GROMACS fails; by definition, the system, topology, and force field have 
> already been checked for integrity.
> 
> -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] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Hi Justin,

I try to use the CHARMM-GUI files directly. My purpose is simulating the water 
and ci-pinonic system. Cis-pionic molecules will stay on the water surface and 
I would like to estimate surface tension reduction. 

What should I change in CHARMM-GUI files?
> 
> CHARMM-GUI provides a self-contained force field file that will have 
> everything you need. It is a subset of the full CHARMM force field plus any 
> parameters that are newly introduced by your non-standard molecule.  Are you 
> using only files directly from CHARMM-GUI, without modification, or are you 
> trying to do something else?
> 
> -Justin
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[gmx-users] CHARMM-GUI files give error in Gromacs

[gozde ergin]

Dear all,

I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid.
After that I used genbox command of gromacs and add some water molecules.
When I try to run I get 100 Errors saying : 

No default bond types, No default U-B types, No default Proper Dih. types, No 
default Improper Dih. types.

All these errors are related to .itp file. However .itp files seems correct:

Any help would be appreciated. Thanks.


;;
;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; j712l...@ku.edu or won...@ku.edu
;;
;; GROMACS topology file for LIG
;;


[ moleculetype ]
; name  nrexcl
LIG  3

[ atoms ]
; nrtyperesnr   residu  atomcgnrcharge  mass
 1 CG3C41  1  LIG C2  1 -0.08712.0110   ; qtot 
-0.087
 2 CG3C41  1  LIG C1  2 -0.04612.0110   ; qtot 
-0.133
 3   HGA1  1  LIG H1  3  0.090 1.0080   ; qtot 
-0.043
 4 CG3C41  1  LIG C3  4 -0.03812.0110   ; qtot 
-0.081
 5  CG2O5  1  LIG C8  5  0.38812.0110   ; qtot  
0.307
 6   HGA1  1  LIG H2  6  0.090 1.0080   ; qtot  
0.397
 7  OG2D3  1  LIG O1  7 -0.48115.9994   ; qtot 
-0.084
 8  CG331  1  LIGC10  8 -0.22912.0110   ; qtot 
-0.313
 9   HGA3  1  LIGH14  9  0.090 1.0080   ; qtot 
-0.223
10   HGA3  1  LIGH15 10  0.090 1.0080   ; qtot 
-0.133
11   HGA3  1  LIGH13 11  0.090 1.0080   ; qtot 
-0.043
12 CG3C41  1  LIG C4 12 -0.17812.0110   ; qtot 
-0.221
13   HGA2  1  LIG H4 13  0.090 1.0080   ; qtot 
-0.131
14   HGA2  1  LIG H3 14  0.090 1.0080   ; qtot 
-0.041
15  CG331  1  LIG C6 15 -0.24812.0110   ; qtot 
-0.289
16   HGA3  1  LIGH10 16  0.090 1.0080   ; qtot 
-0.199
17   HGA3  1  LIG H9 17  0.090 1.0080   ; qtot 
-0.109
18   HGA3  1  LIG H8 18  0.090 1.0080   ; qtot 
-0.019
19  CG331  1  LIG C5 19 -0.24812.0110   ; qtot 
-0.267
20   HGA3  1  LIG H6 20  0.090 1.0080   ; qtot 
-0.177
21   HGA3  1  LIG H7 21  0.090 1.0080   ; qtot 
-0.087
22   HGA3  1  LIG H5 22  0.090 1.0080   ; qtot  
0.003
23  CG321  1  LIG C7 23 -0.20712.0110   ; qtot 
-0.204
24  CG2O2  1  LIG C9 24  0.80312.0110   ; qtot  
0.599
25   HGA2  1  LIGH12 25  0.090 1.0080   ; qtot  
0.689
26   HGA2  1  LIGH11 26  0.090 1.0080   ; qtot  
0.779
27  OG2D1  1  LIG O3 27 -0.57615.9994   ; qtot  
0.203
28  OG311  1  LIG O2 28 -0.63215.9994   ; qtot 
-0.429
29   HGP1  1  LIGH16 29  0.429 1.0080   ; qtot  
0.000

[ bonds ]
; aiaj  funct   b0  Kb
1 2 1
1 3 1
112 1
123 1
2 4 1
215 1
219 1
4 5 1
4 6 1
412 1
5 7 1
5 8 1
8 9 1
810 1
811 1
   1213 1
   1214 1
   1516 1
   1517 1
   1518 1
   1920 1
   1921 1
   1922 1
   2324 1
   2325 1
   2326 1
   2427 1
   2428 1
   2829 1

[ pairs ]
; aiaj  funct   c6  c12
1 2 1 
1 5 1 
1 6 1 
112 1 
116 1 
117 1 
118 1 
120 1 
121 1 
122 1 
127 1 
128 1 
2 4 1 
2 7 1 
2 8 1 
213 1 
214 1 
224 1 
225 1 
226 1 
3 4 1 
313 1 
314 1 
315 1 
319 1 
324 1 
325 1 
326 1 
4 9 1 
410 1 
411 1 
412 1 
416 1 
417 1 
418 1 
420 1 
421 1 
422 1 
423 1 
513 1 
514 1 
515 1 
519 1 
6 7 1 
6 8 1 
613 1 
614 1 
615 1 
619 1 
7 9 1 
710 1 
711 1 
712 1 
812 1 
   1215 1 
   1219 1 
   1224 1 
   1225 1 
   1226 

Re: [gmx-users] Free energy calculation, Methane in water tutorial

[gozde ergin]

The error is pretty clear. Do you produce the min0.tpr file?
Where do you put this file? Is it in the same directory of job.sh file?

> On 02 Sep 2016, at 13:09, Sun Iba  wrote:
> 
> Hello dear users
> 
> I am following Justin's tutorial for free energy calculation of Methane in
> water. I have downloaded the job.sh file and trying to run it in terminal
> using: sh job.sh but it is giving following error:
> 
> Program mdrun, VERSION 5.0
> Source code file:
> /home/corona2/Downloads/gromacs-5.0/src/gromacs/fileio/gmxfio.c, line: 513
> 
> Can not open file:
> min0.tpr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> Please help me with error.
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Re: [gmx-users] SHAKE error

[gozde ergin]

No I am using same Gromacs 4.6.5. 
I run these two simulations again one runs and the other fails with the same 
.mdp file.

> On 22 Jul 2016, at 13:53, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 7/22/16 7:50 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I use md-vv and SHAKE algorithm however I face an error which I was not 
>> before.
>> Before I had 1-decanol and water system and now I have cis-pionic and water 
>> system.
>> 
>> I exactly use the same .mdp file just as before however this error comes :
>> SHAKE is not supported with domain decomposition and constraint that cross 
>> charge group boundaries, use LINCS
>> 
>> Do you have any idea why I am getting this error which I was not getting 
>> before?
>> 
> 
> Probably you were using a different version of the code before.  Various 
> feature combinations get disabled as suitable tests are not run or bugs are 
> found. LINCS is more stable, anyway, so just use it instead and the run 
> should work.
> 
> -Justin
> 
>> MDP FILE:
>> 
>> 
>> integrator   = md-vv
>> dt   = 0.002
>> nsteps   = 800   ; 16 ns
>> ; Output control
>> nstxout  = 2000
>> nstvout  = 2000
>> nstlog   = 2000
>> nstenergy= 2000
>> ; Bond parameters
>> continuation = no; Initial simulation
>> constraint_algorithm = shake ; holonomic constraints
>> constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
>> constrained
>> shake_tol= 0.0001
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cels
>> nstlist = 5 ; 10 fs
>> rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range 
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>> ; Temperature coupling
>> ; tcoupl is implicitly handled by the sd integrator
>> tcoupl   = nose-hoover
>> tc-grps  = System
>> tau_t= 1.0
>> ref_t= 300
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; Velocity generation is on
>> gen_temp= 300   ; temperature for velocity generation
>> gen_seed= -1; random seed
>> ; COM motion removal
>> ; These options remove COM motion of the system
>> nstcomm = 10
>> comm-mode   = Linear
>> comm-grps   = System
>> 
>> 
>> 
>> thanks
>> 
> 
> -- 
> ==
> 
> 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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[gmx-users] SHAKE error

[gozde ergin]

Dear all,

I use md-vv and SHAKE algorithm however I face an error which I was not before. 
Before I had 1-decanol and water system and now I have cis-pionic and water 
system.

I exactly use the same .mdp file just as before however this error comes : 
SHAKE is not supported with domain decomposition and constraint that cross 
charge group boundaries, use LINCS

Do you have any idea why I am getting this error which I was not getting before?

MDP FILE: 


integrator   = md-vv 
dt   = 0.002
nsteps   = 800   ; 16 ns
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no; Initial simulation 
constraint_algorithm = shake ; holonomic constraints 
constraints  = all-bonds ; all bonds (even heavy atom-H bonds) 
constrained
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tcoupl   = nose-hoover
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System 



thanks
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Re: [gmx-users] md-vv and md

[gozde ergin]

Dear all,

I am using md-vv integrator in 5.1 and still get this all bulk moving problem.
Before I was using 4.6 and informed that this dribble is fixed 5.1 however I 
still got the same problem.
My bulk is moving in z direction however if I use md integrator I do not face 
with this problem.
Any idea?
> On 18 Jul 2015, at 04:13, Michael Shirts  wrote:
> 
>> Has problem been solved about molecules drifting in md-vv integrator?
> 
> We think so, but some additional tests are running to address any
> other lingering integrator issues.  The fix is in 5.1 beta, but not in
> the 4.6 branch yet (it's a pull request, but not yet merged).
> 
>> Also can you please check my potential energy second pic in
>> http://imgur.com/6aJkRoQ#0
>> . 
>> What could be the reason this big jump in potential energy (integrator :
>> md-vv)?
>> And why I do not see the same jump by using md integrator?
> 
> I don't think there's sufficient information here to answer that question.
> -- 
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Re: [gmx-users] Average simulation time for correct surface tension

[gozde ergin]

Maybe this is better 

https://imgur.com/hLFbjS8 <https://imgur.com/hLFbjS8>





> On 18 Jul 2016, at 17:40, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Thanks Justin,
> 
> Here is the plot for the average of 1ns chunks of time (with error) 
> 
> https://imgur.com/FPmxysO <https://imgur.com/FPmxysO>
> 
> It is hard to tell.
> 
> 
>> On 18 Jul 2016, at 16:18, Justin Lemkul <jalem...@vt.edu 
>> <mailto:jalem...@vt.edu>> wrote:
>> 
>> 
>> 
>> On 7/18/16 10:16 AM, gozde ergin wrote:
>>> Seems there is no systematic drift and trend but fluctuating is, please see 
>>> on
>>> http://imgur.com/Vfs0wqw <http://imgur.com/Vfs0wqw> 
>>> <http://imgur.com/Vfs0wqw <http://imgur.com/Vfs0wqw>>
>>> 
>> 
>> This is not what I suggested.  The raw time series shows lots of noise.  
>> What happens when you plot the average of 1-ns chunks of time (with error 
>> bars), e.g. 0-1, 1-2, 2-3, etc?  This helps you to determine if there are 
>> systematic changes.
>> 
>>>> How did you decide that this division of time was appropriate?
>>> 
>>> This is exactly my question how can I decide the simulation time is enough 
>>> or not. Also this surface tension value is not correct either.
>>> It should be around 1000-1100 not 1244 bar nm.
>>> 
>> 
>> Well, this could be any number of things: insufficient sampling, poor 
>> topology, system size, etc.
>> 
>> -Justin
>> 
>>> 
>>> On 18 Jul 2016, at 16:06, Justin Lemkul <jalem...@vt.edu 
>>> <mailto:jalem...@vt.edu>> wrote:
>>>> 
>>>> 
>>>> 
>>>> On 7/18/16 6:07 AM, gozde ergin wrote:
>>>>> Dear users,
>>>>> 
>>>>> I am trying to estimate the surface tension of cis-pinonic covered water 
>>>>> surfaces.
>>>>> Li. et al 2010 did the same thing and his simulation time was 2 ns.
>>>>> On the other hand there are some other studies mentioned that simulation 
>>>>> time should be long around 200 ns because surface tension is difficult to 
>>>>> estimate accurately, since fluctuations are large and convergence is slow 
>>>>> (Engin et. al 2010).
>>>>> 
>>>>> I would like to give a an example below. I simulated the system for 20 
>>>>> ns. First 6 ns is for equilibration and last 14 ns sampling.
>>>>> 
>>>> 
>>>> How did you decide that this division of time was appropriate?
>>>> 
>>>>> For first 6 ns :
>>>>> 
>>>>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>>>>> ---
>>>>> #Surf*SurfTen   1181.02 222327.0932.8309  
>>>>> (bar nm)
>>>>> 
>>>>> For last 14 ns:
>>>>> 
>>>>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>>>>> ---
>>>>> #Surf*SurfTen   1244.15 102339.36-63.287  
>>>>> (bar nm)
>>>>> 
>>>>> RMSD is larger than Average value so i am confused how long should I run?
>>>>> 
>>>> 
>>>> What happens if you plot your results in 1-ns chunks of time?  Any 
>>>> systematic drift or trend?
>>>> 
>>>> -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 
>>>> <mailto:jalem...@outerbanks.umaryland.edu> | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul 
>>>> <http://mackerell.umaryland.edu/~jalemkul>
>>>> 
>>>> ==
>>>> --
>>>> Gromacs Users mailing list
>>>> 
>>>> * Please search the archive at 
>>>> http://www.gromacs.org/Support

Re: [gmx-users] Average simulation time for correct surface tension

[gozde ergin]

Thanks Justin,

Here is the plot for the average of 1ns chunks of time (with error) 

https://imgur.com/FPmxysO <https://imgur.com/FPmxysO>

It is hard to tell.


> On 18 Jul 2016, at 16:18, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 7/18/16 10:16 AM, gozde ergin wrote:
>> Seems there is no systematic drift and trend but fluctuating is, please see 
>> on
>> http://imgur.com/Vfs0wqw <http://imgur.com/Vfs0wqw> 
>> <http://imgur.com/Vfs0wqw <http://imgur.com/Vfs0wqw>>
>> 
> 
> This is not what I suggested.  The raw time series shows lots of noise.  What 
> happens when you plot the average of 1-ns chunks of time (with error bars), 
> e.g. 0-1, 1-2, 2-3, etc?  This helps you to determine if there are systematic 
> changes.
> 
>>> How did you decide that this division of time was appropriate?
>> 
>> This is exactly my question how can I decide the simulation time is enough 
>> or not. Also this surface tension value is not correct either.
>> It should be around 1000-1100 not 1244 bar nm.
>> 
> 
> Well, this could be any number of things: insufficient sampling, poor 
> topology, system size, etc.
> 
> -Justin
> 
>> 
>> On 18 Jul 2016, at 16:06, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 7/18/16 6:07 AM, gozde ergin wrote:
>>>> Dear users,
>>>> 
>>>> I am trying to estimate the surface tension of cis-pinonic covered water 
>>>> surfaces.
>>>> Li. et al 2010 did the same thing and his simulation time was 2 ns.
>>>> On the other hand there are some other studies mentioned that simulation 
>>>> time should be long around 200 ns because surface tension is difficult to 
>>>> estimate accurately, since fluctuations are large and convergence is slow 
>>>> (Engin et. al 2010).
>>>> 
>>>> I would like to give a an example below. I simulated the system for 20 ns. 
>>>> First 6 ns is for equilibration and last 14 ns sampling.
>>>> 
>>> 
>>> How did you decide that this division of time was appropriate?
>>> 
>>>> For first 6 ns :
>>>> 
>>>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>>>> ---
>>>> #Surf*SurfTen   1181.02 222327.0932.8309  (bar 
>>>> nm)
>>>> 
>>>> For last 14 ns:
>>>> 
>>>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>>>> ---
>>>> #Surf*SurfTen   1244.15 102339.36-63.287  (bar 
>>>> nm)
>>>> 
>>>> RMSD is larger than Average value so i am confused how long should I run?
>>>> 
>>> 
>>> What happens if you plot your results in 1-ns chunks of time?  Any 
>>> systematic drift or trend?
>>> 
>>> -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
>>> 
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>>> 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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441

Re: [gmx-users] Average simulation time for correct surface tension

[gozde ergin]

Seems there is no systematic drift and trend but fluctuating is, please see on 
 http://imgur.com/Vfs0wqw <http://imgur.com/Vfs0wqw>

> How did you decide that this division of time was appropriate?

This is exactly my question how can I decide the simulation time is enough or 
not. Also this surface tension value is not correct either. 
It should be around 1000-1100 not 1244 bar nm.


On 18 Jul 2016, at 16:06, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 7/18/16 6:07 AM, gozde ergin wrote:
>> Dear users,
>> 
>> I am trying to estimate the surface tension of cis-pinonic covered water 
>> surfaces.
>> Li. et al 2010 did the same thing and his simulation time was 2 ns.
>> On the other hand there are some other studies mentioned that simulation 
>> time should be long around 200 ns because surface tension is difficult to 
>> estimate accurately, since fluctuations are large and convergence is slow 
>> (Engin et. al 2010).
>> 
>> I would like to give a an example below. I simulated the system for 20 ns. 
>> First 6 ns is for equilibration and last 14 ns sampling.
>> 
> 
> How did you decide that this division of time was appropriate?
> 
>> For first 6 ns :
>> 
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>> ---
>> #Surf*SurfTen   1181.02 222327.0932.8309  (bar 
>> nm)
>> 
>> For last 14 ns:
>> 
>> Energy  Average   Err.Est.   RMSD  Tot-Drift
>> ---
>> #Surf*SurfTen   1244.15 102339.36-63.287  (bar 
>> nm)
>> 
>> RMSD is larger than Average value so i am confused how long should I run?
>> 
> 
> What happens if you plot your results in 1-ns chunks of time?  Any systematic 
> drift or trend?
> 
> -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] Average simulation time for correct surface tension

[gozde ergin]

Dear users,

I am trying to estimate the surface tension of cis-pinonic covered water 
surfaces.
Li. et al 2010 did the same thing and his simulation time was 2 ns.
On the other hand there are some other studies mentioned that simulation time 
should be long around 200 ns because surface tension is difficult to estimate 
accurately, since fluctuations are large and convergence is slow (Engin et. al 
2010).

I would like to give a an example below. I simulated the system for 20 ns. 
First 6 ns is for equilibration and last 14 ns sampling.

For first 6 ns :

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
#Surf*SurfTen   1181.02 222327.0932.8309  (bar nm)

For last 14 ns: 

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
#Surf*SurfTen   1244.15 102339.36-63.287  (bar nm)

RMSD is larger than Average value so i am confused how long should I run?

Thanks
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Re: [gmx-users] Surface tension calculation for organic monolayer

[gozde ergin]

Yes but my acid is in protonated form.
> On 13 Jul 2016, at 17:42, Evan Lowry <evanwlo...@gmail.com> wrote:
> 
> Dr. van der Spoel is correct. If you don't take into account the
> protonation state, your calculation may likely be incorrect. The pH can
> have a notable effect on interfacial/surfactant systems.
> 
> Evan L.
> Dear Spoel,
> 
> I am using the protonated form of cis-pinonic acid which means head group
> is COOH.
> I tried many other surface active molecules but never manage to estimate
> the lower surface tension than water.
> Is there anyone here that did the MD simulations with surface active
> molecules on water and estimated the reduced surface tension?
> Any suggestion would be really helpful.
> I tried some other force field (GAFF, AMBER, OPLSAA) but results did not
> change.
> I am doing something wrong but I do not know what.
> 
> 
>> On 07 Jul 2016, at 17:51, gozde ergin <gozdeeer...@gmail.com> wrote:
>> 
>> Dear Spoel,
>> Thanks for your respond.
>> For this simulations I used acids however I got the similar results when
> I used alcohol (pK values are lower than acids).
>> I doubt this error coming from the pH effects.
>> But how could i get the protonated molecules configuration?
>>> On 07 Jul 2016, at 17:11, David van der Spoel <sp...@xray.bmc.uu.se>
> wrote:
>>> 
>>> On 07/07/16 16:06, gozde ergin wrote:
>>>> Dear users,
>>>> 
>>>> I simulated three different systems in cubic box and calculated their
> surface tension as shown below;
>>>> 
>>>> 1. Pure water , surface tension = 61.5 mN/m
>>>> 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m
>>>> 3.Water surface covered with cis-pinonic organic, surface tension =
> 63.5 mN/m
>>>> 
>>>> For system 1 and 2, the results are almost correct however the result
> for system 3 is not correct.
>>>> 
>>>> Cis-pionic is an surface active molecule and should lower the surface
> tension.
>>>> However in my simulations I could not capture this trend.
>>>> I used GAFF force field and LINCS for the constraints.
>>>> Does anyone has any idea?
>>>> Or is there anyone that calculated the surface tension for organic
> coated surfaces with GAFF force field?
>>>> 
>>>> Thanks
>>>> 
>>> Maybe you should consider pH effects? Since this is an acid I would
> guess part of these are deprotonated in solution, did you consider the pK?
> You probably need to mix different amounts of protonated and deprotonated
> molecules and plot the surface tension as a function of the protonation
> state.
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:   +46184714205.
>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>> --
>>> 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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> send a mail to gmx-users-requ...@gromacs.org.
>> 
> 
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Re: [gmx-users] Surface tension calculation for organic monolayer

[gozde ergin]

Dear Spoel,

I am using the protonated form of cis-pinonic acid which means head group is 
COOH. 
I tried many other surface active molecules but never manage to estimate the 
lower surface tension than water.
Is there anyone here that did the MD simulations with surface active molecules 
on water and estimated the reduced surface tension?
Any suggestion would be really helpful.
I tried some other force field (GAFF, AMBER, OPLSAA) but results did not change.
I am doing something wrong but I do not know what.


> On 07 Jul 2016, at 17:51, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Dear Spoel,
> Thanks for your respond.
> For this simulations I used acids however I got the similar results when I 
> used alcohol (pK values are lower than acids).
> I doubt this error coming from the pH effects. 
> But how could i get the protonated molecules configuration?
>> On 07 Jul 2016, at 17:11, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
>> 
>> On 07/07/16 16:06, gozde ergin wrote:
>>> Dear users,
>>> 
>>> I simulated three different systems in cubic box and calculated their 
>>> surface tension as shown below;
>>> 
>>> 1. Pure water , surface tension = 61.5 mN/m
>>> 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m
>>> 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 
>>> mN/m
>>> 
>>> For system 1 and 2, the results are almost correct however the result for 
>>> system 3 is not correct.
>>> 
>>> Cis-pionic is an surface active molecule and should lower the surface 
>>> tension.
>>> However in my simulations I could not capture this trend.
>>> I used GAFF force field and LINCS for the constraints.
>>> Does anyone has any idea?
>>> Or is there anyone that calculated the surface tension for organic coated 
>>> surfaces with GAFF force field?
>>> 
>>> Thanks
>>> 
>> Maybe you should consider pH effects? Since this is an acid I would guess 
>> part of these are deprotonated in solution, did you consider the pK? You 
>> probably need to mix different amounts of protonated and deprotonated 
>> molecules and plot the surface tension as a function of the protonation 
>> state.
>> 
>> -- 
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:   +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>> -- 
>> 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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>> mail to gmx-users-requ...@gromacs.org.
> 

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Re: [gmx-users] Restart corrupted run

[gozde ergin]

> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations 
> 
It explains the restart procedure for version 4 and newer.

> On 13 Jul 2016, at 12:01, Mehrnoosh Hazrati  
> wrote:
> 
> Hi all,
> 
> how can I restart a MD run that stopped before finishing the calculations?
> 
> I know about the solution in previous versions of Gromacs, but now I'm
> working with Gromacs 5.1.2.
> 
> Thank you in advance.
> 
> Mehrnoosh
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Re: [gmx-users] Surface tension calculation for organic monolayer

[gozde ergin]

Dear Spoel,
Thanks for your respond.
For this simulations I used acids however I got the similar results when I used 
alcohol (pK values are lower than acids).
I doubt this error coming from the pH effects. 
But how could i get the protonated molecules configuration?
> On 07 Jul 2016, at 17:11, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
> 
> On 07/07/16 16:06, gozde ergin wrote:
>> Dear users,
>> 
>> I simulated three different systems in cubic box and calculated their 
>> surface tension as shown below;
>> 
>> 1. Pure water , surface tension = 61.5 mN/m
>> 2. Water with 3M NaCl salt, surface tension = 66.5 mN/m
>> 3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m
>> 
>> For system 1 and 2, the results are almost correct however the result for 
>> system 3 is not correct.
>> 
>> Cis-pionic is an surface active molecule and should lower the surface 
>> tension.
>> However in my simulations I could not capture this trend.
>> I used GAFF force field and LINCS for the constraints.
>> Does anyone has any idea?
>> Or is there anyone that calculated the surface tension for organic coated 
>> surfaces with GAFF force field?
>> 
>> Thanks
>> 
> Maybe you should consider pH effects? Since this is an acid I would guess 
> part of these are deprotonated in solution, did you consider the pK? You 
> probably need to mix different amounts of protonated and deprotonated 
> molecules and plot the surface tension as a function of the protonation state.
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> -- 
> Gromacs Users mailing list
> 
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[gmx-users] Surface tension calculation for organic monolayer

[gozde ergin]

Dear users,

I simulated three different systems in cubic box and calculated their surface 
tension as shown below;

1. Pure water , surface tension = 61.5 mN/m
2. Water with 3M NaCl salt, surface tension = 66.5 mN/m
3.Water surface covered with cis-pinonic organic, surface tension = 63.5 mN/m

For system 1 and 2, the results are almost correct however the result for 
system 3 is not correct.

Cis-pionic is an surface active molecule and should lower the surface tension. 
However in my simulations I could not capture this trend. 
I used GAFF force field and LINCS for the constraints. 
Does anyone has any idea? 
Or is there anyone that calculated the surface tension for organic coated 
surfaces with GAFF force field? 

Thanks
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Re: [gmx-users] Topology include file " " not found

[gozde ergin]

Ok I found the error. I put “cis-pinonic.itp” instead of ”cis-pinonic.itp”. The 
problem is quote.

On 26 Apr 2016, at 13:35, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> I checked it and there is no #include statement in cis-pinonic.itp file.
>> On 26 Apr 2016, at 13:24, Justin Lemkul <jalem...@vt.edu> wrote:
>> 
>> 
>> 
>> On 4/26/16 5:57 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I am trying to simulate organic system.
>>> Here is my tool.top file, and cis-pionic,its is in the same folder with the 
>>> tool.top.
>>> 
>>> ;
>>> ; Topology from .mol2 file
>>> ; topolbuild
>>> ;
>>> ; The force field files to be included
>>> #include "charmm27.ff/forcefield.itp"
>>> 
>>> ; Include chain topologies
>>> #include “cis-pinonic.itp"
>>> 
>>> ; Include water topology
>>> #include "charmm27.ff/tip3p.itp"
>>> 
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ;  i funct   fcxfcyfcz
>>>   11   1000   1000   1000
>>> #endif
>>> 
>>> ; Include topology for ions
>>> #include "charmm27.ff/ions.itp"
>>> 
>>> [ system ]
>>> ; title from mol2 input
>>> LIG
>>> 
>>> [ molecules ]
>>> ; molecule namenr.
>>> cis-pinonic   64
>>> 
>>> 
>>> When I try to minimize the system this is the error that I’m getting,
>>> 
>>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
>>> 
>>> Fatal error:
>>> Topology include file "   " not found
>>> For more information and tips for troubleshooting, please check the GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> 
>>> What is that mean?
>>> I thought maybe there is an invisible line so I did also dos2unix however 
>>> the error is still there.
>>> 
>> 
>> Are there any #include statements within your .itp files (e.g. 
>> cis-pinonic.itp) that might be triggering this?
>> 
>> -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
>> 
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>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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> 

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Re: [gmx-users] Topology include file " " not found

[gozde ergin]

I checked it and there is no #include statement in cis-pinonic.itp file.
>  On 26 Apr 2016, at 13:24, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 4/26/16 5:57 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I am trying to simulate organic system.
>> Here is my tool.top file, and cis-pionic,its is in the same folder with the 
>> tool.top.
>> 
>> ;
>> ; Topology from .mol2 file
>> ; topolbuild
>> ;
>> ; The force field files to be included
>> #include "charmm27.ff/forcefield.itp"
>> 
>> ; Include chain topologies
>> #include “cis-pinonic.itp"
>> 
>> ; Include water topology
>> #include "charmm27.ff/tip3p.itp"
>> 
>> #ifdef POSRES_WATER
>> ; Position restraint for each water oxygen
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>>11   1000   1000   1000
>> #endif
>> 
>> ; Include topology for ions
>> #include "charmm27.ff/ions.itp"
>> 
>>  [ system ]
>> ; title from mol2 input
>> LIG
>> 
>>  [ molecules ]
>> ; molecule namenr.
>>  cis-pinonic   64
>> 
>> 
>> When I try to minimize the system this is the error that I’m getting,
>> 
>> grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr
>> 
>> Fatal error:
>> Topology include file "   " not found
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> What is that mean?
>> I thought maybe there is an invisible line so I did also dos2unix however 
>> the error is still there.
>> 
> 
> Are there any #include statements within your .itp files (e.g. 
> cis-pinonic.itp) that might be triggering this?
> 
> -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
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[gmx-users] Topology include file " " not found

[gozde ergin]

Dear all,

I am trying to simulate organic system.
Here is my tool.top file, and cis-pionic,its is in the same folder with the 
tool.top.

;
; Topology from .mol2 file
; topolbuild
;
; The force field files to be included
#include "charmm27.ff/forcefield.itp"

; Include chain topologies
#include “cis-pinonic.itp"   

; Include water topology
#include "charmm27.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "charmm27.ff/ions.itp"

 [ system ]
; title from mol2 input
LIG

 [ molecules ]
; molecule namenr.
 cis-pinonic   64


When I try to minimize the system this is the error that I’m getting,

grompp -f minim.mdp  -c lig.gro -p topol.top -o em.tpr

Fatal error:
Topology include file "   " not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

What is that mean? 
I thought maybe there is an invisible line so I did also dos2unix however the 
error is still there.
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Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Is refcoord_scaling the issue for also NVT simulation? 
Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT.

> On 19 Apr 2016, at 14:06, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> On 4/19/16 6:15 AM, gozde ergin wrote:
>> This is my posre.itp file;
>> 
>> [ position_restraints ]
>> ; i  funct   gr(nm)   k
>>   1 252.4 4184
>>   2 252.4 4184
>> 
>> My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
>> the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 
>> 4.8-2.4=2.4nm
>> This step is working without any problem.
>> 
>> Than I use the command of;
>> 
>> gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy
>> 
>> I extract all ions z-coordinate of the ions.
>> Than I use the equation in Roux2010 paper in order to estimate the osmotic 
>> pressure which is,
>> 
>>  = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation 
>> only the ions who have passed the wall.
>>  = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)
>> 
>> Fwall = (Fwall1 + Fwall2)/2
>> P = /Area
>> 
>> However I get *very* different results than Roux2010. Even though our 
>> temperature, non-bond settings, system size etc are the same.
>> 
>> Has anyone here done simulations to calculate the osmotic pressure and/or 
>> osmotic coefficient?
>> Any suggestion?
> 
> You may want to try this in CHARMM or NAMD, where it is quite honestly much 
> easier.  All the specifications in GROMACS are relative to the initial 
> configuration, and then there's refcoord_scaling to deal with, so I'm not 
> 100% sure that this is as straightforward as it seems.  In CHARMM and NAMD, 
> the positions of the walls are set explicitly and it is very straightforward 
> to do these calculations.
> 
>> 
>> Also Roux2010 mentioned that the force of the wall is *half harmonic* , what 
>> is the force in gromacs for flat-bottom restraint?
>> 
> 
> It's the same.  This just means there's a harmonic potential at the wall.  
> The flat-bottom restraint says "apply a restraint potential if z > some 
> value" and since there's a second restraint that applies a force if z < some 
> value, each restraint covers half of a harmonic potential.
> 
> -Justin
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Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

This is my posre.itp file;

[ position_restraints ]
; i  funct   gr(nm)   k   
  1 252.4 4184
  2 252.4 4184

My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of 
the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
This step is working without any problem.

Than I use the command of;

gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy

I extract all ions z-coordinate of the ions. 
Than I use the equation in Roux2010 paper in order to estimate the osmotic 
pressure which is,

 = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only 
the ions who have passed the wall.
 = [k (1/N)sum(N) sum(i)(| zi-zwall2 |) 

Fwall = (Fwall1 + Fwall2)/2
P = /Area

However I get *very* different results than Roux2010. Even though our 
temperature, non-bond settings, system size etc are the same.

Has anyone here done simulations to calculate the osmotic pressure and/or 
osmotic coefficient?
Any suggestion?

Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is 
the force in gromacs for flat-bottom restraint?


> On 07 Apr 2016, at 21:37, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 4/7/16 12:57 PM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I just want to ask how is the r(nm) in posre.itp working?
>> 
>> I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
>> box.
>> 
>> When I write 2.4 in the r(nm) property for [position_restraints] in 
>> posre.itp, it seems all of the molecules that I apply flat-bottom restraint 
>> travel +/- 2.4 nm.
> 
> This is expected.  The flat-bottom potential is established with respect to 
> the reference coordinates.
> 
>> But I do not want this, I would like to put a wall or force on +/-2.4 nm in 
>> z of the box.
>> Do you have any advice about this?
>> 
> 
> If you want walls at given z-values, the z-coordinate of species to which the 
> restraint is applied have to be set to zero.  This coordinate file is passed 
> to grompp -r as the reference point for the potential.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 21 Mar 2016, at 18:37, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 3/21/16 1:29 PM, gozde ergin wrote:
>>>> Ok this was a silly question.
>>>> In g_energy command 5. one is flat-bottom posres force.
>>>> Sorry.
>>>> 
>>> 
>>> The output of g_energy is energy, not force.
>>> 
>>> But the quantity is simple to calculate.  If you have applied a flat-bottom 
>>> restraint along z, then you just need the time series of the z-coordinates 
>>> of the restrained particles.
>>> 
>>> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint 
>>> is active.  Since there are two walls, then you need to conditions, for +/- 
>>> z0 and then the final sum should be divided by 2 before being divided by 
>>> the area of the semipermeable wall.
>>> 
>>> -Justin
>>> 
>>>>> On 21 Mar 2016, at 17:26, gozde ergin <gozdeeer...@gmail.com> wrote:
>>>>> 
>>>>> Hey Justin,
>>>>> 
>>>>> I am just wondering in order to estimate the osmotic pressure I need 
>>>>> extract the flat-bottom restraint force. (Force/Area = Pressure)
>>>>> Do you have any idea to how to extract this force?
>>>>> 
>>>>> Thanks in advance
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10 Mar 2016, at 15:58, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>>>>>> Dear Justin,
>>>>>>> 
>>>>>>> Thanks for your respond, I assume there is a way to apply this 
>>>>>>> restraint on specific molecules.
>>>>>>> Because my system is mixed with organic and water and I would like to 
>>>>>>> apply these forces on organic molecules not water?
>>>>>>> 
>>>>>> 
>>>>>> So apply flat-bottom restraints to whatever the organic molecules are.  
>>>>>> It's not something specific to ions.  You set the restraints in the 
>>>>>> molecule's topology (in its [moleculetype]), construct a reference 
>>>>>> coordinate file that defines some unphysical coordinates to be used as 
>>>>>> the center of the re

Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hey Justin, 

These result was with Parinello-Rahman.
Here is the  setting for T and P coupling;

; Temperature coupling
tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Parrinello-Rahman   
pcoupltype  = semiisotropic 
tau_p   = 2.0 2.0 
ref_p   = 150.0 1.0 
compressibility = 0 4.5e-5
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= no   

> On 18 Apr 2016, at 15:48, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 4/18/16 4:43 AM, gozde ergin wrote:
>> In Roux study they did 10 independent 1.5 ns production simulation and I did 
>> 15 ns simulation and divided it to 10 1.5ns simulations.
>> 
>> Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
>>   Roux study 300(+/- 10  bar)
>>   Experiment 300 bar
> 
> Your fluctuation seems unreasonably low.  Is this still with Berendsen?  If 
> so, repeat it using Parrinello-Rahman for the barostat.  This result should 
> be quite reproducible when using the method described exactly in the paper.
> 
> -Justin

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Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Mark,

I guess so because a lot of studies cite this study also their results are 
almost identical with the experimental one.

> On 18 Apr 2016, at 10:46, Mark Abraham  wrote:
> 
> Are they known to produce these observables accurately

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Re: [gmx-users] Osmotic pressure

[gozde ergin]

In Roux study they did 10 independent 1.5 ns production simulation and I did 15 
ns simulation and divided it to 10 1.5ns simulations.

Osmotic pressure for 5M : My result 216.8 (+/- 0.2 bar)
  Roux study 300(+/- 10  bar)
  Experiment 300 bar
> On 18 Apr 2016, at 10:29, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> 
> Hi,
> 
> What statistical error do you (and they) measure? How many replicates have
> each of you done?
> 
> Mark
> 
> On Mon, 18 Apr 2016 10:25 gozde ergin <gozdeeer...@gmail.com> wrote:
> 
>> Hi Justin,
>> 
>> I corrected the nonbonded settings as your suggestion ;
>> 
>> ; Bond parameters
>> continuation = no
>> constraint_algorithm = shake
>> constraints  = h-bonds
>> shake_tol= 0.0001
>> cutoff-scheme = Verlet
>> vdwtype = cutoff
>> vdw-modifier = force-switch
>> rvdw-switch = 1.0
>> ; Neighborsearching
>> ns_type = grid
>> nstlist = 5
>> rlist   = 1.2
>> rcoulomb= 1.2
>> rvdw= 1.2
>> 
>> However my osmotic pressure result is still far from the Luo 2010
>> study.
>> I have the same number of Na Cl ions and water molecules. I run the
>> simulation for 15ns.
>> System size is the same, water model and force field are the same as Roux
>> study.
>> Basically I should get the same result.
>> Here is the result,
>> 
>> Osmotic pressure for 5M : My result 217 bar
>>  Roux study ~300 bar
>> 
>> Any suggestions would be appreciated.
>> 
>>> On 15 Apr 2016, at 11:50, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 4/15/16 5:20 AM, gozde ergin wrote:
>>>> Dear all,
>>>> 
>>>> I simulate the NaCl solution to estimate the osmotic pressure. My salt
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
>> molecules.
>>>> I use CHARMM36 ff with NBFIX correction.
>>>> 
>>>> After the simulation I extract the z-coordinates of restraint ions and
>> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
>> pressure.
>>>> Actually I try to get the similar results as Lou 2010 study.
>>>> 
>>>> However my osmotic pressure results are on the line of ideal solution
>> osmotic pressure as shown equation in below;
>>>> 
>>>> P = cRT (Van’t Hoff equation)
>>>> 
>>>> but not the similar result with experiments.
>>>> 
>>> 
>>> What values do you actually get?  How do they compare with the values
>> from the Roux paper?  Are you remembering to divide by 2*area in your
>> calculation (since you have two walls)?
>>> 
>>>> Is there anyone here that get the same trend as me for osmotic pressure
>> calculation? Or is there something that I miss?
>>>> 
>>>> 
>>>> Here is my .mdp file;
>>>> 
>>>> define   = -DPOSRES
>>>> integrator   = md
>>>> dt   = 0.002
>>>> nsteps   = 250   ;
>>>> ; Output control
>>>> nstxout  = 2000
>>>> nstvout  = 2000
>>>> nstlog   = 2000
>>>> nstenergy= 2000
>>>> ; Bond parameters
>>>> continuation = no;
>>>> constraint_algorithm = shake ; h
>>>> constraints  = all-bonds ; a
>>>> shake_tol= 0.0001
>>>> ; Neighborsearching
>>>> ns_type = grid  ;
>>>> nstlist = 5 ;
>>>> rlist   = 1.1   ;
>>>> rcoulomb= 1.1   ;
>>>> rvdw= 1.1   ;
>>> 
>>> These nonbonded settings are wrong.  The values for CHARMM36 are well
>> established and you should not deviate from them.
>>> 
>>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM <
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>
>>> 
>>> -Justin
>>> 
>>>> ; Electrostatics
>>>> coulombtype = PME   ;
>>>> pme_order   = 4 ;
>>>> fourierspacing  = 0.16  ;
>>>> 
>>>> tcoupl   = berendsen
>>>> tc-grps

Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Justin,

I corrected the nonbonded settings as your suggestion ; 

; Bond parameters
continuation = no   
constraint_algorithm = shake 
constraints  = h-bonds 
shake_tol= 0.0001
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
; Neighborsearching
ns_type = grid
nstlist = 5 
rlist   = 1.2   
rcoulomb= 1.2 
rvdw= 1.2  

However my osmotic pressure result is still far from the Luo 2010 study.
I have the same number of Na Cl ions and water molecules. I run the simulation 
for 15ns.
System size is the same, water model and force field are the same as Roux 
study. 
Basically I should get the same result.
Here is the result,

Osmotic pressure for 5M : My result 217 bar
  Roux study ~300 bar

Any suggestions would be appreciated.

> On 15 Apr 2016, at 11:50, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 4/15/16 5:20 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I simulate the NaCl solution to estimate the osmotic pressure. My salt 
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the 
>> molecules.
>> I use CHARMM36 ff with NBFIX correction.
>> 
>> After the simulation I extract the z-coordinates of restraint ions and use 
>> the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic 
>> pressure.
>> Actually I try to get the similar results as Lou 2010 study.
>> 
>> However my osmotic pressure results are on the line of ideal solution 
>> osmotic pressure as shown equation in below;
>> 
>> P = cRT (Van’t Hoff equation)
>> 
>> but not the similar result with experiments.
>> 
> 
> What values do you actually get?  How do they compare with the values from 
> the Roux paper?  Are you remembering to divide by 2*area in your calculation 
> (since you have two walls)?
> 
>> Is there anyone here that get the same trend as me for osmotic pressure 
>> calculation? Or is there something that I miss?
>> 
>> 
>> Here is my .mdp file;
>> 
>> define   = -DPOSRES
>> integrator   = md
>> dt   = 0.002
>> nsteps   = 250   ;
>> ; Output control
>> nstxout  = 2000
>> nstvout  = 2000
>> nstlog   = 2000
>> nstenergy= 2000
>> ; Bond parameters
>> continuation = no;
>> constraint_algorithm = shake ; h
>> constraints  = all-bonds ; a
>> shake_tol= 0.0001
>> ; Neighborsearching
>> ns_type = grid  ;
>> nstlist = 5 ;
>> rlist   = 1.1   ;
>> rcoulomb= 1.1   ;
>> rvdw= 1.1   ;
> 
> These nonbonded settings are wrong.  The values for CHARMM36 are well 
> established and you should not deviate from them.
> 
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM 
> <http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM>
> 
> -Justin
> 
>> ; Electrostatics
>> coulombtype = PME   ;
>> pme_order   = 4 ;
>> fourierspacing  = 0.16  ;
>> 
>> tcoupl   = berendsen
>> tc-grps  = System
>> tau_t= 1.0
>> ref_t= 300
>> ; Pressure coupling is on
>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
>> coupling
>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box 
>> vectors
>> tau_p   = 2.0 2.0  ; time constant, in ps
>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
>> compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
>> refcoord_scaling= com
>> ; Periodic boundary conditions
>> pbc = xyz   ; 3-D PBC
>> ; Dispersion correction
>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes   ; Velocity generation is on
>> gen_temp= 300   ; temperature for velocity generation
>> gen_seed= -1; random seed
>> ; COM motion removal
>> ; These options remove COM motion of the system
>> nstcomm = 10
>> comm-mode   = Linear
>> comm-grps   = System
>> 
>> 
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph

Re: [gmx-users] position restrain energy

[gozde ergin]

You defined in .top file as POSRES_Protein so in .mdp file you should call as   
  define  = -DPOSRES_Protein. 
The names in .top and .mdp should match


On 18 Apr 2016, at 08:46, Nikhil Maroli  wrote:
> 
> Dear all,
> i wanted to include position restrain to cyclic peptide nanotube c-alpha
> atoms,i have generated posre_cpn.itp file and added
> define  = -DPOSRES
> 
> in mdp file.
> and added in  .top as
> 
> #ifdef POSRES_Protein
> #include "posre_cpn.itp"
> #endif
> 
> 
> when i check with gmx energy i couldnt find an option for position restrain
> energy ,is my restrain is working ?!
> is it possible to know whether restrain is working or required increase
> before completing the full 100ns MD?
> 
> -- 
> Ragards,
> Nikhil Maroli
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Re: [gmx-users] on force field for ligand

[gozde ergin]

Hi Brett,

If you have all the necessary .itp files and if your .top file is generated 
correctly, yes it works.

> On 18 Apr 2016, at 09:23, Brett  wrote:
> 
> Dear All,
> 
> 
> Does GROMACS work if the force field for ligand part is GAFF force field?
> 
> 
> Brett
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Re: [gmx-users] Osmotic pressure

[gozde ergin]

Hi Mark,

I use Berendsen for T and P-coupl.
Do you think I should change them?

> On 15 Apr 2016, at 11:55, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> 
> Hi,
> 
> Also you can choose coupling algorithms that are known to sample correct
> ensembles...
> 
> Mark
> 
> On Fri, 15 Apr 2016 11:50 Justin Lemkul <jalem...@vt.edu> wrote:
> 
>> 
>> 
>> On 4/15/16 5:20 AM, gozde ergin wrote:
>>> Dear all,
>>> 
>>> I simulate the NaCl solution to estimate the osmotic pressure. My salt
>> concentrations are 3,4 and 5M. I apply flat-bottom restraint to the
>> molecules.
>>> I use CHARMM36 ff with NBFIX correction.
>>> 
>>> After the simulation I extract the z-coordinates of restraint ions and
>> use the equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic
>> pressure.
>>> Actually I try to get the similar results as Lou 2010 study.
>>> 
>>> However my osmotic pressure results are on the line of ideal solution
>> osmotic pressure as shown equation in below;
>>> 
>>> P = cRT (Van’t Hoff equation)
>>> 
>>> but not the similar result with experiments.
>>> 
>> 
>> What values do you actually get?  How do they compare with the values from
>> the
>> Roux paper?  Are you remembering to divide by 2*area in your calculation
>> (since
>> you have two walls)?
>> 
>>> Is there anyone here that get the same trend as me for osmotic pressure
>> calculation? Or is there something that I miss?
>>> 
>>> 
>>> Here is my .mdp file;
>>> 
>>> define   = -DPOSRES
>>> integrator   = md
>>> dt   = 0.002
>>> nsteps   = 250   ;
>>> ; Output control
>>> nstxout  = 2000
>>> nstvout  = 2000
>>> nstlog   = 2000
>>> nstenergy= 2000
>>> ; Bond parameters
>>> continuation = no;
>>> constraint_algorithm = shake ; h
>>> constraints  = all-bonds ; a
>>> shake_tol= 0.0001
>>> ; Neighborsearching
>>> ns_type = grid  ;
>>> nstlist = 5 ;
>>> rlist   = 1.1   ;
>>> rcoulomb= 1.1   ;
>>> rvdw= 1.1   ;
>> 
>> These nonbonded settings are wrong.  The values for CHARMM36 are well
>> established and you should not deviate from them.
>> 
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>> 
>> -Justin
>> 
>>> ; Electrostatics
>>> coulombtype = PME   ;
>>> pme_order   = 4 ;
>>> fourierspacing  = 0.16  ;
>>> 
>>> tcoupl   = berendsen
>>> tc-grps  = System
>>> tau_t= 1.0
>>> ref_t= 300
>>> ; Pressure coupling is on
>>> pcoupl  = Berendsen ; Pressure coupling on in NPT, also
>> weak coupling
>>> pcoupltype  = semiisotropic ; uniform scaling of x-y-z box
>> vectors
>>> tau_p   = 2.0 2.0  ; time constant, in ps
>>> ref_p   = 1.0 1.0  ; reference pressure (in bar)
>>> compressibility = 0 4.5e-5; isothermal compressibility,
>> bar^-1
>>> refcoord_scaling= com
>>> ; Periodic boundary conditions
>>> pbc = xyz   ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr= EnerPres  ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel = yes   ; Velocity generation is on
>>> gen_temp= 300   ; temperature for velocity generation
>>> gen_seed= -1; random seed
>>> ; COM motion removal
>>> ; These options remove COM motion of the system
>>> nstcomm = 10
>>> comm-mode   = Linear
>>> comm-grps   = System
>>> 
>>> 
>> 
>> --
>> ==
>> 
>> 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

[gmx-users] Osmotic pressure

[gozde ergin]

Dear all,

I simulate the NaCl solution to estimate the osmotic pressure. My salt 
concentrations are 3,4 and 5M. I apply flat-bottom restraint to the molecules.
I use CHARMM36 ff with NBFIX correction.

After the simulation I extract the z-coordinates of restraint ions and use the 
equation P = F/A , F= k(zi-zwall), A=area to estimate the osmotic pressure.
Actually I try to get the similar results as Lou 2010 study.

However my osmotic pressure results are on the line of ideal solution osmotic 
pressure as shown equation in below; 

P = cRT (Van’t Hoff equation) 

but not the similar result with experiments. 

Is there anyone here that get the same trend as me for osmotic pressure 
calculation? Or is there something that I miss?


Here is my .mdp file;

define   = -DPOSRES
integrator   = md 
dt   = 0.002
nsteps   = 250   ; 
; Output control
nstxout  = 2000
nstvout  = 2000
nstlog   = 2000
nstenergy= 2000
; Bond parameters
continuation = no; 
constraint_algorithm = shake ; h
constraints  = all-bonds ; a
shake_tol= 0.0001
; Neighborsearching
ns_type = grid  ; 
nstlist = 5 ; 
rlist   = 1.1   ; 
rcoulomb= 1.1   ; 
rvdw= 1.1   ; 
; Electrostatics
coulombtype = PME   ; 
pme_order   = 4 ; 
fourierspacing  = 0.16  ; 

tcoupl   = berendsen
tc-grps  = System
tau_t= 1.0
ref_t= 300
; Pressure coupling is on
pcoupl  = Berendsen ; Pressure coupling on in NPT, also weak 
coupling
pcoupltype  = semiisotropic ; uniform scaling of x-y-z box vectors
tau_p   = 2.0 2.0  ; time constant, in ps
ref_p   = 1.0 1.0  ; reference pressure (in bar)
compressibility = 0 4.5e-5; isothermal compressibility, bar^-1
refcoord_scaling= com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; Velocity generation is on
gen_temp= 300   ; temperature for velocity generation
gen_seed= -1; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm = 10
comm-mode   = Linear
comm-grps   = System 


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Re: [gmx-users] CHARMM36 ff with NBFIX in grimaces

[gozde ergin]

Thanks Justin.

In order to validate the results from Luo and Roux 2010 study, I need to run 
the simulations with and without NBFIX.
But thank you very much for your respond, I appreciate it.


> On 12 Apr 2016, at 13:25, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 4/12/16 5:35 AM, gozde ergin wrote:
>> Dear all,
>> 
>> I try to simulate the salt solution by using charmm36 ff in gromacs.
>> I downloaded charmm36.ff from MacKerell web page.
>> 
>> 
>> forcefield.to file ;
>> 
>> ; This force field generated by charmm2gmx.py from
>> ; multiple charmm parameter files
>> ; and multiple charmm topology files
>> #define _FF_CHARMM
>> 
>> ; This gromacs version created from:
>> ; CHARMM parameters: multiple files
>> ; CHARMM topology: multiple files
>> [ defaults ]
>> ; nbfunc comb-rule   gen-pairs   fudgeLJ fudgeQQ
>> 12   yes 1.0 1.0
>> 
>> #include "ffnonbonded.itp"
>> #include "ffbonded.itp"
>> #include "gb.itp"
>> #include "cmap.itp"
>> #include “nbfix.itp"
>> 
>> So the last line is nbfix.itp so I assume this force filed comes with 
>> non-bonded fix parameter.
>> But if I want to simulate without NBFIX parameter should I remove this line?
>> 
> 
> You can, but I don't know why you'd want to.  The NBFIXes are considered 
> integral parts of the force field.  If you take them out, you'll risk 
> spurious ion pairing, incorrect osmotic pressure and diffusion, etc. not to 
> mention incorrect interactions among some biomolecules.
> 
> -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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
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[gmx-users] CHARMM36 ff with NBFIX in grimaces

[gozde ergin]

Dear all,

I try to simulate the salt solution by using charmm36 ff in gromacs.
I downloaded charmm36.ff from MacKerell web page. 


forcefield.to file ;

; This force field generated by charmm2gmx.py from
; multiple charmm parameter files 
; and multiple charmm topology files
#define _FF_CHARMM

; This gromacs version created from:
; CHARMM parameters: multiple files
; CHARMM topology: multiple files
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 1.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
#include “nbfix.itp"

So the last line is nbfix.itp so I assume this force filed comes with 
non-bonded fix parameter. 
But if I want to simulate without NBFIX parameter should I remove this line?

Thanks

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Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Yes it worked. 
I appreciated to your help Justin.
Thanks a lot.

> On 07 Apr 2016, at 21:37, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 4/7/16 12:57 PM, gozde ergin wrote:
>> Hi Justin,
>> 
>> I just want to ask how is the r(nm) in posre.itp working?
>> 
>> I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
>> box.
>> 
>> When I write 2.4 in the r(nm) property for [position_restraints] in 
>> posre.itp, it seems all of the molecules that I apply flat-bottom restraint 
>> travel +/- 2.4 nm.
> 
> This is expected.  The flat-bottom potential is established with respect to 
> the reference coordinates.
> 
>> But I do not want this, I would like to put a wall or force on +/-2.4 nm in 
>> z of the box.
>> Do you have any advice about this?
>> 
> 
> If you want walls at given z-values, the z-coordinate of species to which the 
> restraint is applied have to be set to zero.  This coordinate file is passed 
> to grompp -r as the reference point for the potential.
> 
> -Justin
> 
>> Thanks in advance.
>> 
>> 
>>> On 21 Mar 2016, at 18:37, Justin Lemkul <jalem...@vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 3/21/16 1:29 PM, gozde ergin wrote:
>>>> Ok this was a silly question.
>>>> In g_energy command 5. one is flat-bottom posres force.
>>>> Sorry.
>>>> 
>>> 
>>> The output of g_energy is energy, not force.
>>> 
>>> But the quantity is simple to calculate.  If you have applied a flat-bottom 
>>> restraint along z, then you just need the time series of the z-coordinates 
>>> of the restrained particles.
>>> 
>>> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint 
>>> is active.  Since there are two walls, then you need to conditions, for +/- 
>>> z0 and then the final sum should be divided by 2 before being divided by 
>>> the area of the semipermeable wall.
>>> 
>>> -Justin
>>> 
>>>>> On 21 Mar 2016, at 17:26, gozde ergin <gozdeeer...@gmail.com> wrote:
>>>>> 
>>>>> Hey Justin,
>>>>> 
>>>>> I am just wondering in order to estimate the osmotic pressure I need 
>>>>> extract the flat-bottom restraint force. (Force/Area = Pressure)
>>>>> Do you have any idea to how to extract this force?
>>>>> 
>>>>> Thanks in advance
>>>>> 
>>>>> 
>>>>> 
>>>>>> On 10 Mar 2016, at 15:58, Justin Lemkul <jalem...@vt.edu> wrote:
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>>>>>> Dear Justin,
>>>>>>> 
>>>>>>> Thanks for your respond, I assume there is a way to apply this 
>>>>>>> restraint on specific molecules.
>>>>>>> Because my system is mixed with organic and water and I would like to 
>>>>>>> apply these forces on organic molecules not water?
>>>>>>> 
>>>>>> 
>>>>>> So apply flat-bottom restraints to whatever the organic molecules are.  
>>>>>> It's not something specific to ions.  You set the restraints in the 
>>>>>> molecule's topology (in its [moleculetype]), construct a reference 
>>>>>> coordinate file that defines some unphysical coordinates to be used as 
>>>>>> the center of the restraint, and that's it.  I've described the process 
>>>>>> in detail before so check the archive.
>>>>>> 
>>>>>> -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
>>>>>> 
>>>>>> ==
>>>>>> 

Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Hi Justin,

I just want to ask how is the r(nm) in posre.itp working?

I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the 
box.

When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, 
it seems all of the molecules that I apply flat-bottom restraint travel +/- 2.4 
nm.
But I do not want this, I would like to put a wall or force on +/-2.4 nm in z 
of the box.
Do you have any advice about this?

Thanks in advance.


> On 21 Mar 2016, at 18:37, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 3/21/16 1:29 PM, gozde ergin wrote:
>> Ok this was a silly question.
>> In g_energy command 5. one is flat-bottom posres force.
>> Sorry.
>> 
> 
> The output of g_energy is energy, not force.
> 
> But the quantity is simple to calculate.  If you have applied a flat-bottom 
> restraint along z, then you just need the time series of the z-coordinates of 
> the restrained particles.
> 
> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is 
> active.  Since there are two walls, then you need to conditions, for +/- z0 
> and then the final sum should be divided by 2 before being divided by the 
> area of the semipermeable wall.
> 
> -Justin
> 
>>> On 21 Mar 2016, at 17:26, gozde ergin <gozdeeer...@gmail.com> wrote:
>>> 
>>> Hey Justin,
>>> 
>>> I am just wondering in order to estimate the osmotic pressure I need 
>>> extract the flat-bottom restraint force. (Force/Area = Pressure)
>>> Do you have any idea to how to extract this force?
>>> 
>>> Thanks in advance
>>> 
>>> 
>>> 
>>>> On 10 Mar 2016, at 15:58, Justin Lemkul <jalem...@vt.edu> wrote:
>>>> 
>>>> 
>>>> 
>>>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>>>> Dear Justin,
>>>>> 
>>>>> Thanks for your respond, I assume there is a way to apply this restraint 
>>>>> on specific molecules.
>>>>> Because my system is mixed with organic and water and I would like to 
>>>>> apply these forces on organic molecules not water?
>>>>> 
>>>> 
>>>> So apply flat-bottom restraints to whatever the organic molecules are.  
>>>> It's not something specific to ions.  You set the restraints in the 
>>>> molecule's topology (in its [moleculetype]), construct a reference 
>>>> coordinate file that defines some unphysical coordinates to be used as the 
>>>> center of the restraint, and that's it.  I've described the process in 
>>>> detail before so check the archive.
>>>> 
>>>> -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.
>>> 
>> 
> 
> -- 
> ==
> 
> 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 <mailto:jalem...@outerbanks.umaryland.edu> 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==
> -- 
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[gmx-users] Inorganic ammonium sulphate with CHARMM force field

[gozde ergin]

Hi everybody,

I would like o run ammonium sulphate solution with CHARMM force field in 
GROMACS.
pdb2gmx is not working because the residue type is LIG.
I tried to use swissparam and paramchem website however both do not support the 
inorganic sulphate and ammonium explicitly.
Is there any other easy way to get the ammonium sulphate input parameters with 
CHARMM force field for Gromacs ?

Thanks in advance.
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Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Ok this was a silly question. 
In g_energy command 5. one is flat-bottom posres force.
Sorry.

> On 21 Mar 2016, at 17:26, gozde ergin <gozdeeer...@gmail.com> wrote:
> 
> Hey Justin,
> 
> I am just wondering in order to estimate the osmotic pressure I need extract 
> the flat-bottom restraint force. (Force/Area = Pressure)
> Do you have any idea to how to extract this force?
> 
> Thanks in advance
> 
> 
> 
>> On 10 Mar 2016, at 15:58, Justin Lemkul <jalem...@vt.edu> wrote:
>> 
>> 
>> 
>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>> Dear Justin,
>>> 
>>> Thanks for your respond, I assume there is a way to apply this restraint on 
>>> specific molecules.
>>> Because my system is mixed with organic and water and I would like to apply 
>>> these forces on organic molecules not water?
>>> 
>> 
>> So apply flat-bottom restraints to whatever the organic molecules are.  It's 
>> not something specific to ions.  You set the restraints in the molecule's 
>> topology (in its [moleculetype]), construct a reference coordinate file that 
>> defines some unphysical coordinates to be used as the center of the 
>> restraint, and that's it.  I've described the process in detail before so 
>> check the archive.
>> 
>> -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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>> mail to gmx-users-requ...@gromacs.org.
> 

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Re: [gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Hey Justin,

I am just wondering in order to estimate the osmotic pressure I need extract 
the flat-bottom restraint force. (Force/Area = Pressure)
Do you have any idea to how to extract this force?

Thanks in advance



> On 10 Mar 2016, at 15:58, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
> On 3/10/16 4:44 AM, gozde ergin wrote:
>> Dear Justin,
>> 
>> Thanks for your respond, I assume there is a way to apply this restraint on 
>> specific molecules.
>> Because my system is mixed with organic and water and I would like to apply 
>> these forces on organic molecules not water?
>> 
> 
> So apply flat-bottom restraints to whatever the organic molecules are.  It's 
> not something specific to ions.  You set the restraints in the molecule's 
> topology (in its [moleculetype]), construct a reference coordinate file that 
> defines some unphysical coordinates to be used as the center of the 
> restraint, and that's it.  I've described the process in detail before so 
> check the archive.
> 
> -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] semi-permeable wall in gromacs

[gozde ergin]

Dear Justin,

Thanks for your respond, I assume there is a way to apply this restraint on 
specific molecules. 
Because my system is mixed with organic and water and I would like to apply 
these forces on organic molecules not water?

> On 09 Mar 2016, at 18:30, Justin Lemkul  wrote:
> 
> Use flat-bottom restraints on the ions

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[gmx-users] semi-permeable wall in gromacs

[gozde ergin]

Dear all,

I would like to compute the osmotic pressure directly from all-atom MD 
simulations of concentrated aqueous solutions. 

The basic idea is to introduce “virtual” walls to represent the effect of ideal 
semipermeable membranes, separating a high concentration region from a pure 
water region. 

The walls keep the ions confined, but the water molecules are allowed to pass 
freely, permitting an equalization of their chemical potential throughout the 
entire system. 

The mean force per unit area exerted on the ions by the virtual walls during 
the simulations can be directly related to the osmotic pressure. 



My question is is there a way to introduce semi-permeable walls in GROMACS?

bests
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[gmx-users] Thermal energy

[gozde ergin]

Dear users,

Is there way to extract the thermal energy of the system that simulated in
NVT ensemble?

thanks
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Re: [gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force

[gozde ergin]

Maybe someone has an idea how to extract the instantaneous forces from the
trajectory.
I would normally use g_traj command to extract the forces however I am not
sure if this force means instantaneous force.


On Wed, Nov 25, 2015 at 2:02 PM, gozde ergin <gozdeeer...@gmail.com> wrote:

> Dear gromacs users,
>
> I would like ask a question about the force of umbrella sampling.
> I did umbrella sampling by pulling a water molecule from gas phase to
> organic coated bulk water.
> I estimated the free energy profile on this reaction coordinate.
> In order to calculate the random force-force auto-correlation I need to
> extract the random force on pulled molecule. The force along a reaction
> coordinate consists of three terms, (i) the mean force as the derivative of
> the free energy surface, (ii) friction, and (iii) random force.
> I used gromacs tool g_traj to extract the force on pulled molecule however
> I do not know how to get the random (iii) force out of it.
> I would greatly appreciate it if you kindly give me an advise about a way
> to extract random forces from the overall forces?
>
> Best regards
>
>
>
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[gmx-users] Umbrella sampling force autocorrelation

[gozde ergin]

Dear Gromacs user,

I did umbrella sampling by pulling a water molecule from gas phase to
organic coated bulk water.
By clicking the link below you can see my PMF profile.
In order to estimate the transmission coefficient, I put the pulled
molecule on the top of the PMF barrier and did simulation for 600 ps.
I extracted the instantaneous force of z direction on this molecule by
using the command of :

*g_traj -f traj.trr -s md.tpr -of force.xvg -n index.ndx -nox -noy*

And to estimate the auto-correlation for  instantaneous force:

*g_analyze -f force.xvg -ac auto_corr.xvg -temp 300 -nonormalize*

However I wonder why the fluctuation on auto-correlation is big and never
converges to the zero.
Please find the profile.xvg, force.xvg and auto_corr.xvg on
http://imgur.com/a/IVP5f


I would greatly appreciate of any respond.

Best regards
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[gmx-users] Umbrella sampling and dividing the forces into mean force + friction force + random force

[gozde ergin]

Dear gromacs users,

I would like ask a question about the force of umbrella sampling.
I did umbrella sampling by pulling a water molecule from gas phase to
organic coated bulk water.
I estimated the free energy profile on this reaction coordinate.
In order to calculate the random force-force auto-correlation I need to
extract the random force on pulled molecule. The force along a reaction
coordinate consists of three terms, (i) the mean force as the derivative of
the free energy surface, (ii) friction, and (iii) random force.
I used gromacs tool g_traj to extract the force on pulled molecule however
I do not know how to get the random (iii) force out of it.
I would greatly appreciate it if you kindly give me an advise about a way
to extract random forces from the overall forces?

Best regards
-- 
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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Re: [gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

[gozde ergin]

Hi Mark,

As your suggestion I used cutoff sheme = Verlet with running in Gromacs 5.1
Now instead of decreasing, total energy kept increasing! Do you think this
behavior is normal?

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Kinetic En. 8537.49180386.1221253.25
(kJ/mol)
Potential  -20741.95301092.623652.89
(kJ/mol)
Total Energy   -12204.47101449.394906.14
(kJ/mol)
Temperature 319.9336.714.469546.9643  (K)


Thanks in advance.


On Thu, Nov 5, 2015 at 2:15 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> So that means you are using the group cutoff scheme without a cutoff
> buffer, which is known not to conserve energy (see manual sections on
> neighbour searching). You can either choose a group-scheme model physics
> where the buffer (set with rlist) is suitably larger than the cutoffs
> (which is awkward to set up and will run slowly), or use the Verlet scheme
> (which has a buffer by default and runs fast) which is now default in 5.1.
> Even with that fixed, the use of constraints intrinsically leads to drift,
> also. Whether the remaining drift matters for your simulation (vs the
> decrease in sampling you would have to accept in order to start to deal
> with it) is an open research question.
>
> Mark
>
>
> On Thu, Nov 5, 2015 at 1:23 PM gozde ergin <gozdeeer...@gmail.com> wrote:
>
> > - system 512 water molecule covered by 25 organic on each surface,
> > - I used both gromacs 4.5 and 5.0 with and without double precision
> > - .mdp file is :
> >
> > integrator   = md
> > dt   = 0.002
> > nsteps   = 1000   ; 20 ns
> > nstxout  = 1
> > nstvout  = 1
> > nstlog   = 1
> > nstenergy= 1
> > continuation = no
> > constraint_algorithm = lincs
> > constraints  = all-bonds
> > lincs_iter   = 1
> > lincs_order  = 4
> > ns_type = grid
> > nstlist = 5
> > rlist   = 1.2
> > rcoulomb= 1.2
> > rvdw= 1.2
> > coulombtype = PME
> > pme_order   = 4
> > fourierspacing  = 0.16
> > tcoupl   = nose-hoover
> > tc-grps  = System
> > tau_t= 1.0
> > ref_t= 300
> > Pcoupl   = No
> > pbc = xyz
> > DispCorr= EnerPres
> > gen_vel = yes
> > gen_temp= 310
> > gen_seed= -1
> > nstcomm = 10
> > comm-mode   = Linear
> > comm-grps   = System
> >
> > hope it is readable now!
> >
> > best
> >
> > On Thu, Nov 5, 2015 at 11:44 AM, Mark Abraham <mark.j.abra...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > You're making it very hard to help you, by not providing a readable
> .mdp
> > > file, not specifying a GROMACS version, nor describing what is in your
> > > system. If there was a magic "do this and energy is conserved" button
> > then
> > > it'd be already pushed for you ;-)
> > >
> > > Mark
> > >
> > > On Thu, Nov 5, 2015 at 11:34 AM gozde ergin <gozdeeer...@gmail.com>
> > wrote:
> > >
> > > > Hi Ganesh
> > > >
> > > > I tried your suggestion and this time instead of decreasing,
> potential
> > > and
> > > > kinetic energy kept increasing!
> > > > So still could not get the converged-constant energy for NVE.
> > > >
> > > >
> > > > On Wed, Nov 4, 2015 at 4:23 PM, Ganesh Shahane <
> > ganesh7shah...@gmail.com
> > > >
> > > > wrote:
> > > >
> > > > > Hi Gozde,
> > > > >
> > > > > You could try modifying and introduce some of the parameters as
> > follows
> > > > > (keeping the rest same) -
> > > > >
> > > > > lincs_iter = 2
> > > > > rvdw-switch = 1.1
> > > > > vdwtype = Cut-off
> > > > > vdw-modifier = Force-switch
> > > > >
> > > > > I recently faced some of the same problems as yours and the above
> > > > > parameters worked for me.
> > > > >
> > > > > On Wed, Nov 4, 2015 at 2:47 PM, gozde ergin <gozdeeer...@gmail.com
> >
> > >

Re: [gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

[gozde ergin]

Hi Ganesh

I tried your suggestion and this time instead of decreasing, potential and
kinetic energy kept increasing!
So still could not get the converged-constant energy for NVE.


On Wed, Nov 4, 2015 at 4:23 PM, Ganesh Shahane <ganesh7shah...@gmail.com>
wrote:

> Hi Gozde,
>
> You could try modifying and introduce some of the parameters as follows
> (keeping the rest same) -
>
> lincs_iter = 2
> rvdw-switch = 1.1
> vdwtype = Cut-off
> vdw-modifier = Force-switch
>
> I recently faced some of the same problems as yours and the above
> parameters worked for me.
>
> On Wed, Nov 4, 2015 at 2:47 PM, gozde ergin <gozdeeer...@gmail.com> wrote:
>
> > Dear Chaban,
> >
> > I decreased the time step and also I run by using double precision
> however
> > energy kept decreasing and did not converge.
> >
> > Does anybody has an opinion how to run NVE simulation in Gromacs without
> > energy drifting?
> >
> > Bests
> >
> >
> > On Tue, Nov 3, 2015 at 7:27 PM, Vitaly V. Chaban <vvcha...@gmail.com>
> > wrote:
> >
> > > Decrease the time-step.
> > >
> > >
> > >
> > >
> > > On Tue, Nov 3, 2015 at 3:00 PM, gozde ergin <gozdeeer...@gmail.com>
> > wrote:
> > >
> > > > -- Forwarded message --
> > > > From: gozde ergin <gozdeeer...@gmail.com>
> > > > Date: Tue, Nov 3, 2015 at 5:39 PM
> > > > Subject: NVT to NVE ensemble, energy drifting problem
> > > > To: mailing list Gromacs <gromacs.org_gmx-users@maillist.sys.kth.se>
> > > >
> > > >
> > > > Dear Gromacs user,
> > > >
> > > > I did some simulation in NVT ensemble now I need to switch and do
> some
> > > more
> > > > simulations in NVE ensemble.
> > > > What properties do I need to change in .mdp file to get a good energy
> > > > conversion?
> > > > I used the same properties like NVT without temperature coupling but
> my
> > > > potential and kinetic energy drifted a lot.
> > > > What should I do prevent this drifting?
> > > >
> > > > Here is my nvt.mdp:
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > *integrator   = md dt   =
> > > > 0.002nsteps   = 1000   ; 20 nsnstxout
> > > > = 1nstvout  = 1nstlog   =
> > > > 1nstenergy= 1continuation = no
> > > > constraint_algorithm = lincs  constraints  = all-bonds
> > > > lincs_iter   = 1lincs_order  = 4
> ns_type
> > > > = grid nstlist = 5rlist   =
> > > > 1.2   rcoulomb= 1.2  rvdw=
> > > > 1.2  coulombtype = PMEpme_order   =
> > > > 4 fourierspacing  = 0.16 tcoupl
>  =
> > > > nose-hoovertc-grps  = Systemtau_t
> =
> > > > 1.0ref_t= 300Pcoupl   = Nopbc
>  =
> > > > xyzDispCorr= EnerPres  gen_vel =
> > > > yesgen_temp= 310   gen_seed=
> > > > -1   nstcomm = 10comm-mode   =
> > > > Linearcomm-grps   = System *
> > > > For nve, I just make the temperature coupling off and used the same
> > > > properties however as I mentioned my energy could not converged in 20
> > ns.
> > > >
> > > > Thanks in advance
> > > > --
> > > > 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
> &

Re: [gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

[gozde ergin]

- system 512 water molecule covered by 25 organic on each surface,
- I used both gromacs 4.5 and 5.0 with and without double precision
- .mdp file is :

integrator   = md
dt   = 0.002
nsteps   = 1000   ; 20 ns
nstxout  = 1
nstvout  = 1
nstlog   = 1
nstenergy= 1
continuation = no
constraint_algorithm = lincs
constraints  = all-bonds
lincs_iter   = 1
lincs_order  = 4
ns_type = grid
nstlist = 5
rlist   = 1.2
rcoulomb= 1.2
rvdw= 1.2
coulombtype = PME
pme_order   = 4
fourierspacing  = 0.16
tcoupl   = nose-hoover
tc-grps  = System
tau_t= 1.0
ref_t= 300
Pcoupl   = No
pbc = xyz
DispCorr= EnerPres
gen_vel = yes
gen_temp= 310
gen_seed= -1
nstcomm = 10
comm-mode   = Linear
comm-grps   = System

hope it is readable now!

best

On Thu, Nov 5, 2015 at 11:44 AM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:

> Hi,
>
> You're making it very hard to help you, by not providing a readable .mdp
> file, not specifying a GROMACS version, nor describing what is in your
> system. If there was a magic "do this and energy is conserved" button then
> it'd be already pushed for you ;-)
>
> Mark
>
> On Thu, Nov 5, 2015 at 11:34 AM gozde ergin <gozdeeer...@gmail.com> wrote:
>
> > Hi Ganesh
> >
> > I tried your suggestion and this time instead of decreasing, potential
> and
> > kinetic energy kept increasing!
> > So still could not get the converged-constant energy for NVE.
> >
> >
> > On Wed, Nov 4, 2015 at 4:23 PM, Ganesh Shahane <ganesh7shah...@gmail.com
> >
> > wrote:
> >
> > > Hi Gozde,
> > >
> > > You could try modifying and introduce some of the parameters as follows
> > > (keeping the rest same) -
> > >
> > > lincs_iter = 2
> > > rvdw-switch = 1.1
> > > vdwtype = Cut-off
> > > vdw-modifier = Force-switch
> > >
> > > I recently faced some of the same problems as yours and the above
> > > parameters worked for me.
> > >
> > > On Wed, Nov 4, 2015 at 2:47 PM, gozde ergin <gozdeeer...@gmail.com>
> > wrote:
> > >
> > > > Dear Chaban,
> > > >
> > > > I decreased the time step and also I run by using double precision
> > > however
> > > > energy kept decreasing and did not converge.
> > > >
> > > > Does anybody has an opinion how to run NVE simulation in Gromacs
> > without
> > > > energy drifting?
> > > >
> > > > Bests
> > > >
> > > >
> > > > On Tue, Nov 3, 2015 at 7:27 PM, Vitaly V. Chaban <vvcha...@gmail.com
> >
> > > > wrote:
> > > >
> > > > > Decrease the time-step.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Tue, Nov 3, 2015 at 3:00 PM, gozde ergin <gozdeeer...@gmail.com
> >
> > > > wrote:
> > > > >
> > > > > > -- Forwarded message --
> > > > > > From: gozde ergin <gozdeeer...@gmail.com>
> > > > > > Date: Tue, Nov 3, 2015 at 5:39 PM
> > > > > > Subject: NVT to NVE ensemble, energy drifting problem
> > > > > > To: mailing list Gromacs <
> > gromacs.org_gmx-users@maillist.sys.kth.se>
> > > > > >
> > > > > >
> > > > > > Dear Gromacs user,
> > > > > >
> > > > > > I did some simulation in NVT ensemble now I need to switch and do
> > > some
> > > > > more
> > > > > > simulations in NVE ensemble.
> > > > > > What properties do I need to change in .mdp file to get a good
> > energy
> > > > > > conversion?
> > > > > > I used the same properties like NVT without temperature coupling
> > but
> > > my
> > > > > > potential and kinetic energy drifted a lot.
> > > > > > What should I do prevent this drifting?
> > > > > >
> > > > > > Here is my nvt.mdp:
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
>