[gmx-users] about non-writing issue

[lina]

Hi,

Very sporadically and also with high frequent,

The job I submitted only running without writing (this job is not un-started
one, mainly one I stopped and rerun).

Before I thought I did not wait long enough, such as hours, but seriously
after 3 or 8 hours, still running not writing.

I ssh to each nodes, all is fully running.

The storage is NFS, I/O flow can't be choked for hours.

Really headache, sometimes it works.

I have had no clue about it.


Thanks for any suggestions,


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lina
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[gmx-users] Re: about non-writing issue

[lina]

Hi,

It works now.

Not write (just based on guess) might
the md.log step such as is 1114
while use thread I noticed the actually run step started from 11135000

so I run until it can write to the md.log

then switch to 1 node to run for a while,

then switch to more nodes.

But there might be some reason there which I don't know.

Thanks,

On Sun, Sep 18, 2011 at 4:35 PM, lina  wrote:

> Hi,
>
> Very sporadically and also with high frequent,
>
> The job I submitted only running without writing (this job is not
> un-started one, mainly one I stopped and rerun).
>
> Before I thought I did not wait long enough, such as hours, but seriously
> after 3 or 8 hours, still running not writing.
>
> I ssh to each nodes, all is fully running.
>
> The storage is NFS, I/O flow can't be choked for hours.
>
> Really headache, sometimes it works.
>
> I have had no clue about it.
>
>
> Thanks for any suggestions,
>
>
> --
> Best Regards,
>
> lina
>
>
>


-- 
Best Regards,

lina
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[gmx-users] Questions regarding REMD simulation

[michael zhenin]

Hi All,

I have few questions regarding REMD simulation.

I assume REMD works in the following way: Each replica starts with a given
temperature and the temperature of each replica changes along the simulation
(as described in Sugita and Okamoto publication, 1999). Then demux.pl and
trjcat collect the trajectories of the lowest temperature from each replica.



My problem is that while analyzing the results, I found in the edr
files that the temperatures along each replica are relatively

constant (+- 2K from the starting temperature) and the average temperature
is equal to the initial temperature.


How can this be explained? Does the temperature of each replica change
along the simulation or maybe the temperature of each

simulation stays close to its initial value and the coordinates are changed
between the different replica? (if so, why do i need to use

the post-processing tools such as the demux.pl script?)


Thanks,


Michael
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RE: [gmx-users] Questions regarding REMD simulation

[gal.fradin]

Dear Michael,
First  I want to say thank you very much... for posting you questions here.
I can't help you with this but I wish you Good Luck and that you will find your 
answers soon!
Best wishes,thanks again,
Gal :)

Date: Sun, 18 Sep 2011 14:35:43 +0300
From: mikel...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Questions regarding REMD simulation



Hi All,



I have few questions regarding REMD simulation.



I assume REMD works in the following way: Each replica starts with a given
temperature and the temperature of each replica changes along the
simulation (as described in
Sugita and Okamoto publication, 1999).
Then demux.pl
and trjcat collect the trajectories of the lowest temperature from
each replica.

   

My problem is that while analyzing
the results, I found in the edr files that the temperatures along
each replica are relatively

constant (+- 2K from the
starting temperature) and the average temperature is equal to the initial
temperature.


How can this be explained? Does the
temperature of each replica change along the simulation
or maybe the temperature of each 

simulation stays close
to its initial value and the coordinates are changed between the different
replica? (if so, why do i need to use 

the post-processing tools such as the demux.pl
script?)

Thanks,

Michael






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Re: [gmx-users] Questions regarding REMD simulation

[SebastianWaltz]

Hi,
in the GROMACS implementation of REM the trajectories are exchanged not
the temperatures. The temperatures are kept constant. As well as the
description of the Okamoto paper cited by GROMACS

Basti
 

On 09/18/2011 01:35 PM, michael zhenin wrote:
> Hi All,
>
> I have few questions regarding REMD simulation.
>
> I assume REMD works in the following way: Each replica starts with a given
> temperature and the temperature of each replica changes along the simulation
> (as described in Sugita and Okamoto publication, 1999). Then demux.pl and
> trjcat collect the trajectories of the lowest temperature from each replica.
>
>
>
> My problem is that while analyzing the results, I found in the edr
> files that the temperatures along each replica are relatively
>
> constant (+- 2K from the starting temperature) and the average temperature
> is equal to the initial temperature.
>
>
> How can this be explained? Does the temperature of each replica change
> along the simulation or maybe the temperature of each
>
> simulation stays close to its initial value and the coordinates are changed
> between the different replica? (if so, why do i need to use
>
> the post-processing tools such as the demux.pl script?)
>
>
> Thanks,
>
>
> Michael
>

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[gmx-users] positive Leonard Jones Energy

[Gideon Lapidoth]

Hi all,

I ran g_energy in order to calculate the LJ energy between a pip2
(Phosphatidylinositol
4,5-bisphosphate) molecule and the solvent using GROMACS 4.0.7. the pip2
 molecule is very polar and the avg. coulomb energy value I got between the
ligand and solvent was ~ 3100 KJ. The solvent includes water molecules and
Cl and Na ions to counter the pip2 charge. the production run was done in
npt conditions. the total charge of the pip2 molecule is -6 e. The avg. LJ
energy I got was ~190 KJ.
I am trying make sense of this. could it be that the polar interactions
between the solvent and ligand are so strong that they can influence a
positive LJ energy?
Does anyone have any idea why this could be ?

Thanks,
Gideon
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Re: [gmx-users] positive Leonard Jones Energy

[Mark Abraham]

On 19/09/2011 1:13 AM, Gideon Lapidoth wrote:

Hi all,

I ran g_energy in order to calculate the LJ energy between a pip2 
(Phosphatidylinositol 4,5-bisphosphate) molecule and the 
solvent using GROMACS 4.0.7. the pip2  molecule is very polar and the 
avg. coulomb energy value I got between the ligand and solvent was ~ 
3100 KJ.


An equilibrated condensed-phase system of mixed positive and negative 
charges using a normal biomolecular force field should have negative 
Coulomb PE.


The solvent includes water molecules and Cl and Na ions to counter the 
pip2 charge. the production run was done in npt conditions. the total 
charge of the pip2 molecule is -6 e. The avg. LJ  energy I got was 
~190 KJ.
I am trying make sense of this. could it be that the polar 
interactions between the solvent and ligand are so strong that they 
can influence a positive LJ energy?

Does anyone have any idea why this could be ?


Force fields are parameterized to reproduce certain experimental or 
computational results, in the hope that such reproduction will permit 
simulations using that force field to sample similar chemical ensembles 
with correct frequencies. They're not parameterized such that the 
absolute values of any energies or energy components means anything, and 
one has to work hard to demonstrate anything sensible about energy 
differences, too. What were you hoping to observe?


Mark
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Re: [gmx-users] Questions regarding REMD simulation

[Mark Abraham]

On 18/09/2011 9:35 PM, michael zhenin wrote:


Hi All,

I have few questions regarding REMD simulation.

I assume REMD works in the following way: Each replica starts with a 
given temperature and the temperature of each replica changes 
along the simulation (as described in Sugita and Okamoto publication, 
1999).




As Sebatian noted, in GROMACS the replicas move between simulations and 
the temperature of each simulation is constant. You will see this in the 
temperatures in the .log files. This approach is conceptually identical, 
of course, but there are advantages for doing one or the other when 
writing the code.


Then demux.pl  and trjcat collect the trajectories 
of the lowest temperature from each replica.




They are already present in the lowest-numbered replica trajectory. 
Using demux.pl will be counter-productive - it generates geometrically 
continuous trajectories from ensemble-continuous trajectories (and vice 
versa, I think).


My problem is that while analyzing the results, I found in the edr 
files that the temperatures along each replica are relatively


constant (+- 2K from the starting temperature) and the average 
temperature is equal to the initial temperature.




That's consistent with GROMACS REMD simulating a constant ensemble. You 
can't do demux on the energy files in the current implementation.


Mark



How can this be explained? Does the temperature of each replica change 
along the simulation or maybe the temperature of each


simulation stays close to its initial value and the coordinates are 
changed between the different replica? (if so, why do i need to use


the post-processing tools such as the demux.pl  script?)


Thanks,


Michael





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[gmx-users] RDF - first minimum of O-O

[Steven Neumann]

Hi Gromacs Users,

Can anyone explain me why in g_bond the distance is takes <= 3.5nm. It is
said that it comes from the first minimum o RDF of Oxygen atoms in SPC water
model. I am sorry, but I just do not catch this. Thank you in advance.

Steven
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Re: [gmx-users] RDF - first minimum of O-O

[Mark Abraham]

On 19/09/2011 2:02 AM, Steven Neumann wrote:

Hi Gromacs Users,
Can anyone explain me why in g_bond the distance is takes <= 3.5nm.


If you mean g_hbond, and are using units incorrectly, 0.35nm would be a 
characteristic distance cut-off for deciding whether a hydrogen bond 
might exist


It is said that it comes from the first minimum o RDF of Oxygen atoms 
in SPC water model. I am sorry, but I just do not catch this. Thank 
you in advance.


Said where? About what? :)

Mark

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Re: [gmx-users] RDF - first minimum of O-O

[Steven Neumann]

On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham wrote:

> On 19/09/2011 2:02 AM, Steven Neumann wrote:
>
>> Hi Gromacs Users,
>> Can anyone explain me why in g_bond the distance is takes <= 3.5nm.
>>
>
> If you mean g_hbond, and are using units incorrectly, 0.35nm would be a
> characteristic distance cut-off for deciding whether a hydrogen bond might
> exist
>
> That is what I already know...
>


>
> It is said that it comes from the first minimum o RDF of Oxygen atoms in
>> SPC water model. I am sorry, but I just do not catch this. Thank you in
>> advance.
>>
>
> Said where? About what? :)
>
> Mark
>

About cutoff 0.35 nm. See Manual 4.5.4 - page 213 and Figure 8.3 - RDF of
O-O atoms in SPC water model. Can you explain this 0.35 nm value as a first
minima?

>
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Re: [gmx-users] RDF - first minimum of O-O

[Justin A. Lemkul]

Steven Neumann wrote:



On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham > wrote:


On 19/09/2011 2:02 AM, Steven Neumann wrote:

Hi Gromacs Users,
Can anyone explain me why in g_bond the distance is takes <= 3.5nm.


If you mean g_hbond, and are using units incorrectly, 0.35nm would
be a characteristic distance cut-off for deciding whether a hydrogen
bond might exist

That is what I already know...

 



It is said that it comes from the first minimum o RDF of Oxygen
atoms in SPC water model. I am sorry, but I just do not catch
this. Thank you in advance.


Said where? About what? :)

Mark

 
About cutoff 0.35 nm. See Manual 4.5.4 - page 213 and Figure 8.3 - RDF 
of O-O atoms in SPC water model. Can you explain this 0.35 nm value as a 
first minima?


It's there in Figure 8.3, a shallow minimum at 0.35 nm.  For this to occur, then 
ideally the water molecules are forming H-bonds (O-H...O) with an O-O distance 
of 0.35 nm.  Moreover (and I know I posted this to the list before, so it's in 
the archive in greater detail somewhere), the geometric criteria used by g_hbond 
are generally accepted as indicative of hydrogen bonding from crystallographic 
studies.


-Justin




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] different sets of fudgeQQ and fudgeLJ

[Yun Shi]

Hi Mark,

I don't quite understand what it follows "only one [defaults] section can
exist in an entire topology".

Then how to specify different fudge values for different subsets of
non-bonded interactions?

When defining new atom types, should I always use 'new' atomtypes names? For
example, if the atom type "H2" already exists for part A, then I should use
something different like "H2B" to define similar atomtypes in part B?

But if I can use only one [ defaults ] section, even within different .itp
files under the same .top file, how could I tell the program to apply
different fudge values to H2 as defined in A.itp and H2B as defined in
B.itp?

Thanks,
Yun

Date: Sun, 18 Sep 2011 09:25:38 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] different sets of fudgeQQ and fudgeLJ
To: Discussion list for GROMACS users 
Message-ID: <4e752c72.4040...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 18/09/2011 8:58 AM, Yun Shi wrote:
> Hi all,
>
> I want to apply different values of LJ and QQ scaling factors for two
> interacting molecules A and B. Since I already have the .itp files for
> each molecule, should I just add something like:
>
> [ defaults ]
> ; nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
>12 yes 0.5
>   0.8333
>
> at the very beginning of A.itp and B.itp respectively (the actual
> values are different from this eg.)?
>
> I wonder if .itp file format was designed for this kind of purpose?
> :)  I guess we could even define different sets of atom types for A
> and B, right?

As you will see in the examples in chapter 5, only one [defaults]
section can exist in an entire topology. Further, the fudge values only
apply to a subset of non-bonded interactions. For the kind of
calculation you have in mind, you will need to define new atom types for
the modified interactions.

Mark
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Re: [gmx-users] different sets of fudgeQQ and fudgeLJ

[Justin A. Lemkul]

Yun Shi wrote:

Hi Mark,

I don't quite understand what it follows "only one [defaults] section 
can exist in an entire topology".


Then how to specify different fudge values for different subsets of 
non-bonded interactions?


When defining new atom types, should I always use 'new' atomtypes names? 
For example, if the atom type "H2" already exists for part A, then I 
should use something different like "H2B" to define similar atomtypes in 
part B?


But if I can use only one [ defaults ] section, even within different 
.itp files under the same .top file, how could I tell the program to 
apply different fudge values to H2 as defined in A.itp and H2B as 
defined in B.itp?




The values of fudgeLJ and fudgeQQ are applied to intramolecular 1-4 
interactions, thus they can only be present once in an entire topology.  They 
are global settings.  If you wish to define different 1-4 interactions, then 
define special [pairs], and if you want to use non-default nonbonded 
interactions, then define them in [nonbond_params].  The latter sounds like what 
you want, since it sounds like you want modified intermolecular interactions.


-Justin


Thanks,
Yun

Date: Sun, 18 Sep 2011 09:25:38 +1000
From: Mark Abraham >

Subject: Re: [gmx-users] different sets of fudgeQQ and fudgeLJ
To: Discussion list for GROMACS users >
Message-ID: <4e752c72.4040...@anu.edu.au 
>

Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 18/09/2011 8:58 AM, Yun Shi wrote:
 > Hi all,
 >
 > I want to apply different values of LJ and QQ scaling factors for two
 > interacting molecules A and B. Since I already have the .itp files for
 > each molecule, should I just add something like:
 >
 > [ defaults ]
 > ; nbfunccomb-rule   gen-pairs   fudgeLJ  fudgeQQ
 >12 yes 0.5
 >   0.8333
 >
 > at the very beginning of A.itp and B.itp respectively (the actual
 > values are different from this eg.)?
 >
 > I wonder if .itp file format was designed for this kind of purpose?
 > :)  I guess we could even define different sets of atom types for A
 > and B, right?

As you will see in the examples in chapter 5, only one [defaults]
section can exist in an entire topology. Further, the fudge values only
apply to a subset of non-bonded interactions. For the kind of
calculation you have in mind, you will need to define new atom types for
the modified interactions.

Mark



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] RDF - first minimum of O-O

[Steven Neumann]

On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham 
>> > mark.abra...@anu.edu.**au >> wrote:
>>
>>On 19/09/2011 2:02 AM, Steven Neumann wrote:
>>
>>Hi Gromacs Users,
>>Can anyone explain me why in g_bond the distance is takes <= 3.5nm.
>>
>>
>>If you mean g_hbond, and are using units incorrectly, 0.35nm would
>>be a characteristic distance cut-off for deciding whether a hydrogen
>>bond might exist
>>
>>That is what I already know...
>>
>>
>>
>>It is said that it comes from the first minimum o RDF of Oxygen
>>atoms in SPC water model. I am sorry, but I just do not catch
>>this. Thank you in advance.
>>
>>
>>Said where? About what? :)
>>
>>Mark
>>
>>  About cutoff 0.35 nm. See Manual 4.5.4 - page 213 and Figure 8.3 - RDF of
>> O-O atoms in SPC water model. Can you explain this 0.35 nm value as a first
>> minima?
>>
>
> It's there in Figure 8.3, a shallow minimum at 0.35 nm.  For this to occur,
> then ideally the water molecules are forming H-bonds (O-H...O) with an O-O
> distance of 0.35 nm.  Moreover (and I know I posted this to the list before,
> so it's in the archive in greater detail somewhere), the geometric criteria
> used by g_hbond are generally accepted as indicative of hydrogen bonding
> from crystallographic studies.
>
> -Justin
>
> Thank you Justin. But I  do not get why it is first minimum of RDF? I
thought it has to be first maximum of this function - the highest particle
density?

>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
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>>
>> 
>> >
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>>
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>>
>> >
>> before posting!
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>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>
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>>
>> 
>> >
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
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Re: [gmx-users] RDF - first minimum of O-O

[Justin A. Lemkul]

Steven Neumann wrote:



On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul > wrote:




Steven Neumann wrote:



On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   On 19/09/2011 2:02 AM, Steven Neumann wrote:

   Hi Gromacs Users,
   Can anyone explain me why in g_bond the distance is takes
<= 3.5nm.


   If you mean g_hbond, and are using units incorrectly, 0.35nm
would
   be a characteristic distance cut-off for deciding whether a
hydrogen
   bond might exist

   That is what I already know...

 


   It is said that it comes from the first minimum o RDF of
Oxygen
   atoms in SPC water model. I am sorry, but I just do not catch
   this. Thank you in advance.


   Said where? About what? :)

   Mark

 About cutoff 0.35 nm. See Manual 4.5.4 - page 213 and Figure
8.3 - RDF of O-O atoms in SPC water model. Can you explain this
0.35 nm value as a first minima?


It's there in Figure 8.3, a shallow minimum at 0.35 nm.  For this to
occur, then ideally the water molecules are forming H-bonds
(O-H...O) with an O-O distance of 0.35 nm.  Moreover (and I know I
posted this to the list before, so it's in the archive in greater
detail somewhere), the geometric criteria used by g_hbond are
generally accepted as indicative of hydrogen bonding from
crystallographic studies.

-Justin

Thank you Justin. But I  do not get why it is first minimum of RDF? I 
thought it has to be first maximum of this function - the highest 
particle density?




Right, the minimum defines the cutoff at which hydrogen bonding is less likely. 
 So the hydrogen bonds should all be within 0.35 nm, not occurring at 0.35 nm. 
 Apologies for my somewhat confusing reply earlier, my mind was going faster 
than my typing :)  The O-O distance of 0.35 nm represents an upper bound for a 
hydrogen bond to occur, not that this is the most populated distance for 
hydrogen bonding.


-Justin




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==__==


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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] RDF - first minimum of O-O

[Steven Neumann]

On Sun, Sep 18, 2011 at 7:25 PM, Justin A. Lemkul  wrote:

>
>
> Steven Neumann wrote:
>
>
>>
>> On Sun, Sep 18, 2011 at 5:52 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Steven Neumann wrote:
>>
>>
>>
>>On Sun, Sep 18, 2011 at 5:07 PM, Mark Abraham
>>> > >
>>>>>
>> wrote:
>>
>>   On 19/09/2011 2:02 AM, Steven Neumann wrote:
>>
>>   Hi Gromacs Users,
>>   Can anyone explain me why in g_bond the distance is takes
>><= 3.5nm.
>>
>>
>>   If you mean g_hbond, and are using units incorrectly, 0.35nm
>>would
>>   be a characteristic distance cut-off for deciding whether a
>>hydrogen
>>   bond might exist
>>
>>   That is what I already know...
>>
>>
>>   It is said that it comes from the first minimum o RDF of
>>Oxygen
>>   atoms in SPC water model. I am sorry, but I just do not
>> catch
>>   this. Thank you in advance.
>>
>>
>>   Said where? About what? :)
>>
>>   Mark
>>
>> About cutoff 0.35 nm. See Manual 4.5.4 - page 213 and Figure
>>8.3 - RDF of O-O atoms in SPC water model. Can you explain this
>>0.35 nm value as a first minima?
>>
>>
>>It's there in Figure 8.3, a shallow minimum at 0.35 nm.  For this to
>>occur, then ideally the water molecules are forming H-bonds
>>(O-H...O) with an O-O distance of 0.35 nm.  Moreover (and I know I
>>posted this to the list before, so it's in the archive in greater
>>detail somewhere), the geometric criteria used by g_hbond are
>>generally accepted as indicative of hydrogen bonding from
>>crystallographic studies.
>>
>>-Justin
>>
>> Thank you Justin. But I  do not get why it is first minimum of RDF? I
>> thought it has to be first maximum of this function - the highest particle
>> density?
>>
>>
> Right, the minimum defines the cutoff at which hydrogen bonding is less
> likely.  So the hydrogen bonds should all be within 0.35 nm, not occurring
> at 0.35 nm.  Apologies for my somewhat confusing reply earlier, my mind was
> going faster than my typing :)  The O-O distance of 0.35 nm represents an
> upper bound for a hydrogen bond to occur, not that this is the most
> populated distance for hydrogen bonding.
>
> -Justin
>

Thank you Justin, that helped a lot! Easy explanations makes life very
simple! :)

>
>
>>
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>>
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>>
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>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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>>   
>> 
>>
>> 
>> >>
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>>posting!
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>>> >>.
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>>-- ==**__==
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>
>>

[gmx-users] Deformation of monomer in pulling simulation

[Robert Dole]

Hello all,

I'm trying to pull two peptides (coordinates are from their dimer crystal 
structure) apart using the distance option for the pull geometry and harmonic 
potential using GMX 4.5.3 using OPLS-AA to define the protein and tip3p for the 
water model with NaCl used @ 140 nM for ions. The box is 20 nm long and the 
pulling is done along the longest axis of the cuboid (i.e., Z-direction) such 
that the peptide move much less than half the periodic distance of the box over 
the course of the simulation. I've run the pulling simulation at 0.0005 and 
0.001 nm/ps and with pull_k1 set to 1000 or 5000 to qualitatively see whether a 
higher force constant made a difference (which is doesn't).

As the simulation runs, there is a large deformation of the monomer being 
pulled in which the pulled peptide (initially looks like a "V" with the 
hydrophobic core in the "middle") is stretched. The hydrophobic N-terminal 
stays very close to the reference peptide for the majority of the simulation 
until it finally comes "off" towards the end of the pull run.

I've gone through some of the literature and it seems as though this is an 
expected phenomenon (i.e., deformation of the pulled structure), but the 
deformation is so severe in my case, that it loses ~25-35% of its secondary 
structure! Any suggestions as to how I can remedy this? I thought of using 
distance restraints on the pulled peptide for the pulling simulation after 
which I would remove them for simulations of the windows, but I thought I would 
ask before trying this as I've nearly reached my monthly quota on the HPC 
cluster I work on.

Thanks,

Rob

GROMPP commands:
grompp -f PULL.mdp -c NPT.pdb -p topol.top -n index.ndx -t NPT.trr -o PULL.tpr

MDP options:
integrator= md; leap-frog integrator
nsteps= 500; 10 ns
dt= 0.002; 2 fs
.
.
.
pull= umbrella; notes to self
pull_geometry   = distance  ; simple distance increase 
pull_dim= N N Y; pull peptide B away fromAB in the Z direction 
(the long side of the cuboid)
pull_start  = yes   ; 
pull_ngroups= 1; only one group is getting pulled
pull_group0 = Chain_A 
pull_group1 = Chain_B 
pull_rate1  = 0.0005  ; 0.5 nm per ns = 5 A per nanosecond 
pull_k1 = 5000  ; run 1 - 1000, run 2 - 5000
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Re: [gmx-users] Deformation of monomer in pulling simulation

[Justin A. Lemkul]

Robert Dole wrote:

Hello all,

I'm trying to pull two peptides (coordinates are from their dimer 
crystal structure) apart using the distance option for the pull geometry 
and harmonic potential using GMX 4.5.3 using OPLS-AA to define the 
protein and tip3p for the water model with NaCl used @ 140 nM for ions. 
The box is 20 nm long and the pulling is done along the longest axis of 
the cuboid (i.e., Z-direction) such that the peptide move much less than 
half the periodic distance of the box over the course of the simulation. 
I've run the pulling simulation at 0.0005 and 0.001 nm/ps and with 
pull_k1 set to 1000 or 5000 to qualitatively see whether a higher force 
constant made a difference (which is doesn't).


As the simulation runs, there is a large deformation of the monomer 
being pulled in which the pulled peptide (initially looks like a "V" 
with the hydrophobic core in the "middle") is stretched. The hydrophobic 
N-terminal stays very close to the reference peptide for the majority of 
the simulation until it finally comes "off" towards the end of the pull run.


I've gone through some of the literature and it seems as though this is 
an expected phenomenon (i.e., deformation of the pulled structure), but 
the deformation is so severe in my case, that it loses ~25-35% of its 
secondary structure! Any suggestions as to how I can remedy this? I 
thought of using distance restraints on the pulled peptide for the 
pulling simulation after which I would remove them for simulations of 
the windows, but I thought I would ask before trying this as I've nearly 
reached my monthly quota on the HPC cluster I work on.




I've done this to preserve secondary structure content before.  Distance 
restraints between C-alpha atoms work nicely, though they require you to use 
particle decomposition, so the runs are somewhat slower.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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RE: [gmx-users] radial distribution function

[Dallas Warren]

Does not really matter which one you load up, just one towards the end of the 
trajectory probably so you can be sure it is selected from the "equilibrium" 
state of the system.

Then type "2" when over the  display window with VMD, then click on two atoms.  
VMD will then display a line between the two atoms with a distance in 
Angstroms.  What you want to do is try and work out what the radii mean in the 
polymer system.  It will correspond to a particular structure and arrangement 
of the atoms.  You need to do this with any RDF, so that you can actually work 
out what the peaks actually mean.

The other option is to use a transparent sphere representation of a couple of 
the particular atom types, and adjust it's radius to the various peaks, this 
should make it much easier for the visualisation and identification of the 
structure associated with each peak.

Remember that VMD works in Angstroms and GROMACS in nm.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: Moeed [mailto:lecie...@googlemail.com]
Sent: Saturday, 17 September 2011 1:58 AM
To: Discussion list for GROMACS users
Cc: Dallas Warren; tsje...@gmail.com
Subject: Re: [gmx-users] radial distribution function

Thank you Dr Warren for your comment. I actually still need your help with your 
hint. I am not able to realize how to measure the distances..do I have to look 
at the plot and find the distance shown by the Peaks and then look at the same 
distance in VMD ? But which frames do I have to upload?

Please guide me a little more.

Thank you,
On Thu, Sep 15, 2011 at 6:26 PM, Dallas Warren 
mailto:dallas.war...@monash.edu>> wrote:
Load up some frames into VMD and start measuring the distances shown by the 
peaks in your RDF, link them with what you actually see in there (using 
something like a transparent representation of the carbon atom(s) using VDW 
then set the sphere scale so that it matches the correct radius, may be an 
easier way to do this, but this would make it easy to see).  Appears it may be 
something real, so just check the coordinate file and see where they are 
actually coming from.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Moeed
Sent: Friday, 16 September 2011 12:55 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] radial distribution function

Hello again,

I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a 
longer run from 4 to 30 ns to see whether the small jumps on the plot are due 
to insufficient sampling. Attached is the new plot showing that two RDF curves 
are almost identical. I only wanted to let you know and please comment on the 
attached plot if you have any ideas. Thank you. :)

Moeed
On Sat, Sep 10, 2011 at 10:00 AM, Moeed 
mailto:lecie...@googlemail.com>> wrote:
Thank you for your input. I am going to run for another 15 ns to see if the 
little jumps vanish.

Best,

On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul 
mailto:jalem...@vt.edu>> wrote:


lina wrote:



On Sat, Sep 10, 2011 at 3:35 AM, Moeed 
mailto:lecie...@googlemail.com> 
>> wrote:

   Dear users,

   I have created radial distribution function plot for Carbon atoms in
   a system containing polymer chains. I see some little jumps between
   first and second peak.
   I need your help to comment on how this behavior can be justified
   (or if the plot is wrong).

   g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx -b xxx
   Thank you in advance.


I think your figure is fine.

I think, based on information given in subsequent messages, that there is 
insufficient data collection to assess whether this RDF plot is as meaningful 
as it could be.  There is nothing glaringly wrong, but the roughness is due to 
insufficient sampling.


You just need how to proper interpret your figures, truly understand what the 
"radial distribution" means.


I think it inappropriate to suggest that the OP does not understand the concept 
behind the figure; some guidance, perhaps is necessary, but nothing more.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Black

[gmx-users] Manual Counterion Placement

[Marc Charendoff]

Hello,


I  would like to manually place a counterion into my system with the 
genion command for which I am pretty sure I will need an index file. My 
question 
is how to properly select the specific water atoms / or SOL residue(?)  number 
 (that I get from my pdb or gro file)  so that it comes up as an option when I 
run genion. I looked at the make_ndx options, but they weren't too clear to me. 
Guidance appreciated.

Thanks, Marc-- 
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Re: [gmx-users] Manual Counterion Placement

[Justin A. Lemkul]

Marc Charendoff wrote:

Hello,


I  would like to manually place a counterion into my system with 
the genion command for which I am pretty sure I will need an index file. 
My question is how to properly select the specific water atoms / or SOL 
residue(?)  number  (that I get from my pdb or gro file)  so that it 
comes up as an option when I run genion. I looked at the make_ndx 
options, but they weren't too clear to me. Guidance appreciated.




The only way to do this is to replace one molecule at a time; genion isn't 
designed for such replacements.  Probably the easier method is to use a text 
editor to replace the OW atom with the desired atom and delete the extraneous HW 
atoms.  Otherwise, you have to make an index group for each water to be 
replaced, run grompp and run genion.  The latter is far more work than the former.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Membrane protein simulation

[Sweta Iyer]

Hi,
I embedded my protein of interest into a DMPC membrane by the g_membed tool 
with the following command:
g membed -f input.tpr -p system.top  -n index.ndx -xyinit 0.1 -xyend 1.0 -nxy 
1000 -zinit 1.1 -zend 1.0 -nz 100

I then energy minimized the resultant structure for 1 ns before the position 
restraint dynamics and the productive run.
My structure looks fine after the em. However, when I do the PR and look at the 
structure it looks weird in that half of the protein is hanging out of the 
membrane and there seems to be a patch of water molecules that seem to have 
entered the membrane.

I have no clue what must be possibly going wrong here. Should I have 
equilibrated  the system for longer than 1ns or is it something wrong with the 
membrane insertion.


__
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addressee.
You must not disclose, forward, print or use it without the permission of the 
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Re: [gmx-users] Membrane protein simulation

[Mark Abraham]

On 19/09/2011 9:42 AM, Sweta Iyer wrote:

Hi,
I embedded my protein of interest into a DMPC membrane by the g_membed 
tool with the following command:
g membed -f input.tpr -p system.top  -n index.ndx -xyinit 0.1 -xyend 
1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100


I then energy minimized the resultant structure for 1 ns before the 
position restraint dynamics and the productive run.
My structure looks fine after the em. However, when I do the PR and 
look at the structure it looks weird in that half of the protein is 
hanging out of the membrane and there seems to be a patch of water 
molecules that seem to have entered the membrane.


I have no clue what must be possibly going wrong here. Should I have 
equilibrated  the system for longer than 1ns or is it something wrong 
with the membrane insertion.




Sounds like the advice here might be useful. 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


Mark
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Re: [gmx-users] Membrane protein simulation

[Michael Daily]

Unfortunately genbox will put waters anywhere there is a space, including
inside the membrane.  This can easily be fixed by making a script to remove
waters that are z +/- ~2 nm from the membrane center (you should run
g_density on the system to figure out the optimal distance filter).  You can
run this after running genbox.

On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham wrote:

>  On 19/09/2011 9:42 AM, Sweta Iyer wrote:
>
> Hi,
> I embedded my protein of interest into a DMPC membrane by the g_membed tool
> with the following command:
>  g membed -f input.tpr -p system.top  -n index.ndx -xyinit 0.1 -xyend 1.0
> -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
>
>  I then energy minimized the resultant structure for 1 ns before the
> position restraint dynamics and the productive run.
> My structure looks fine after the em. However, when I do the PR and look at
> the structure it looks weird in that half of the protein is hanging out of
> the membrane and there seems to be a patch of water molecules that seem to
> have entered the membrane.
>
>  I have no clue what must be possibly going wrong here. Should I have
> equilibrated  the system for longer than 1ns or is it something wrong with
> the membrane insertion.
>
>
> Sounds like the advice here might be useful.
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> Mark
>
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-- 

Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
(formerly Qiang Cui group, University of Wisconsin-Madison)
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[gmx-users] opls parameters fir gramicidin terminal groups

[Michael Daily]

Does anyone know where I can find opls-aa parameters for strange peptide
terminal groups, such as the formyl N-terminus and ethanolamine C-terminus
of gramicidin A? I know for charmm you can auto-generate these using
swissparam but I don't know of any equivalent for opls.

Thanks,

-- 

Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
(formerly Qiang Cui group, University of Wisconsin-Madison)
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Re: [gmx-users] Membrane protein simulation

[Justin A. Lemkul]

Michael Daily wrote:
Unfortunately genbox will put waters anywhere there is a space, 
including inside the membrane.  This can easily be fixed by making a 
script to remove waters that are z +/- ~2 nm from the membrane center 
(you should run g_density on the system to figure out the optimal 
distance filter).  You can run this after running genbox.




An even simpler approach is outlined here:

http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox

It seems to me that the original problem either derives from incorrect 
construction, incorrect application of position restraints, or as Mark 
suggested, an artifact of PBC.


-Justin

On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham > wrote:


On 19/09/2011 9:42 AM, Sweta Iyer wrote:

Hi,
I embedded my protein of interest into a DMPC membrane by the
g_membed tool with the following command:
g membed -f input.tpr -p system.top  -n index.ndx -xyinit 0.1
-xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100

I then energy minimized the resultant structure for 1 ns before
the position restraint dynamics and the productive run.
My structure looks fine after the em. However, when I do the PR
and look at the structure it looks weird in that half of the
protein is hanging out of the membrane and there seems to be a
patch of water molecules that seem to have entered the membrane.

I have no clue what must be possibly going wrong here. Should I
have equilibrated  the system for longer than 1ns or is it
something wrong with the membrane insertion.



Sounds like the advice here might be useful.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

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--

Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
(formerly Qiang Cui group, University of Wisconsin-Madison)



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Membrane protein simulation

[Shay Teaching]

Also it is possible that there might be a problem with setting up the
membrane. Have you tried running the membrane without protein?
-Shay
On Sep 19, 2011 3:32 AM, "Justin A. Lemkul"  wrote:
>
>
> Michael Daily wrote:
>> Unfortunately genbox will put waters anywhere there is a space,
>> including inside the membrane. This can easily be fixed by making a
>> script to remove waters that are z +/- ~2 nm from the membrane center
>> (you should run g_density on the system to figure out the optimal
>> distance filter). You can run this after running genbox.
>>
>
> An even simpler approach is outlined here:
>
>
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox
>
> It seems to me that the original problem either derives from incorrect
> construction, incorrect application of position restraints, or as Mark
> suggested, an artifact of PBC.
>
> -Justin
>
>> On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham > > wrote:
>>
>> On 19/09/2011 9:42 AM, Sweta Iyer wrote:
>>> Hi,
>>> I embedded my protein of interest into a DMPC membrane by the
>>> g_membed tool with the following command:
>>> g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1
>>> -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
>>>
>>> I then energy minimized the resultant structure for 1 ns before
>>> the position restraint dynamics and the productive run.
>>> My structure looks fine after the em. However, when I do the PR
>>> and look at the structure it looks weird in that half of the
>>> protein is hanging out of the membrane and there seems to be a
>>> patch of water molecules that seem to have entered the membrane.
>>>
>>> I have no clue what must be possibly going wrong here. Should I
>>> have equilibrated the system for longer than 1ns or is it
>>> something wrong with the membrane insertion.
>>>
>>
>> Sounds like the advice here might be useful.
>>
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>>
>> Mark
>>
>> --
>> gmx-users mailing list gmx-users@gromacs.org
>> 
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org
>> .
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> 
>> Michael D. Daily
>> Postdoctoral research associate
>> Pacific Northwest National Lab (PNNL)
>> 509-375-4581
>> (formerly Qiang Cui group, University of Wisconsin-Madison)
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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Re: [gmx-users] Re: about non-writing issue

[Jianguo Li]

I met the similar problem before, sometimes my job writes output, sometimes 
not. My cluster administrator fixed the problem and they told me that there 
were some problem at some compute nodes which my job unfortunately was 
dispatched to.

Jianguo 





From: lina 
To: Discussion list for GROMACS users 
Sent: Sunday, 18 September 2011 5:13 PM
Subject: [gmx-users] Re: about non-writing issue


Hi,

It works now.

Not write (just based on guess) might 
the md.log step such as is 1114
while use thread I noticed the actually run step started from 11135000

so I run until it can write to the md.log

then switch to 1 node to run for a while,

then switch to more nodes.

But there might be some reason there which I don't know.

Thanks,


On Sun, Sep 18, 2011 at 4:35 PM, lina  wrote:

Hi,
>
>Very sporadically and also with high frequent, 
>
>The job I submitted only running without writing (this job is not un-started 
>one, mainly one I stopped and rerun).
>
>Before I thought I did not wait long enough, such as hours, but seriously 
>after 3 or 8 hours, still running not writing.
>
>I ssh to each nodes, all is fully running.
>
>The storage is NFS, I/O flow can't be choked for hours. 
>
>Really headache, sometimes it works. 
>
>I have had no clue about it. 
>
>
>Thanks for any suggestions,
>
>
>-- 
>Best Regards,
>
>lina
>
>
>


-- 
Best Regards,

lina



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[gmx-users] Re: different sets of fudgeQQ and fudgeLJ

[Yun Shi]

Hi Mark and Justin,

I think I should be more specific here. So i.e., I want to study the
interaction between a protein receptor and a carbohydrate ligand with MD
simulation, and I plan to use ff99sb for protein while glycam06 for
carbohydrate.

Since the two force fields are parameterized using different scaling
factors, I should use different fudge values, although these values will not
DIRECTLY affect inter-molecular interactions.

So how to set this up, if it is possible, within .top file and .itp files?

Thanks,
Yun
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Re: [gmx-users] Re: about non-writing issue

[lina]

On Mon, Sep 19, 2011 at 11:31 AM, Jianguo Li  wrote:

> I met the similar problem before, sometimes my job writes output, sometimes
> not. My cluster administrator fixed the problem and they told me that there 
> were
> some problem at some compute nodes which my job unfortunately was dispatched
> to.
>

Last time I contacted the administrator, he told me it's due to the
restriction he set, I mean, I could only use limited nodes.
He loosed the configuration a bit and it worked at that time.

But later it has happened, I don't have convincing confidence to email root
again.
So just try to figure out slowly.

Thanks for your answering,


>
> Jianguo
>
>
> --
> *From:* lina 
> *To:* Discussion list for GROMACS users 
> *Sent:* Sunday, 18 September 2011 5:13 PM
> *Subject:* [gmx-users] Re: about non-writing issue
>
> Hi,
>
> It works now.
>
> Not write (just based on guess) might
> the md.log step such as is 1114
> while use thread I noticed the actually run step started from 11135000
>
> so I run until it can write to the md.log
>
> then switch to 1 node to run for a while,
>
> then switch to more nodes.
>
> But there might be some reason there which I don't know.
>
> Thanks,
>
> On Sun, Sep 18, 2011 at 4:35 PM, lina  wrote:
>
> Hi,
>
> Very sporadically and also with high frequent,
>
> The job I submitted only running without writing (this job is not
> un-started one, mainly one I stopped and rerun).
>
> Before I thought I did not wait long enough, such as hours, but seriously
> after 3 or 8 hours, still running not writing.
>
> I ssh to each nodes, all is fully running.
>
> The storage is NFS, I/O flow can't be choked for hours.
>
> Really headache, sometimes it works.
>
> I have had no clue about it.
>
>
> Thanks for any suggestions,
>
>
> --
> Best Regards,
>
> lina
>
>
>
>
>
> --
> Best Regards,
>
> lina
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>
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>



-- 
Best Regards,

lina
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[gmx-users] problem with lipid membrane

[Parul tew]

Dear Gmx users,



I am working on a transmembrane protein and my system contains protein, DPPC

bilayer, water (spc) and ions. After adding ions I energy minimized the
system and used trjconv to remove periodicity.  In the equilibration phase
the lipid molecules were entering the voids in the solvent leaving the
protein naked. So, I used position restraint on the Z-plane and restrained the
phosphate head (atom 8) and one carbon atom on each tail (atoms 31, 50 with
a force constant of 1,000 kJ mol*-*1 nm*-*2.

---

; position restraint file for DPPC



[ position_restraints ]

;  i funct   fcxfcyfcz

   81   0   0   1000

  311   0   0   1000

  501   0   0   1000



---

But after running a simulated annealing for 500ps I get a distorted lipid
membrane where the lipids tend to pack at one end but open at the other end
of the box.

After this I had put position restraint on all the atoms of the lipid on the
z-plane and again tried the simulated annealing but it gave the same result.


I am not able to understand where I am going wrong.

Thanks,

Parul Tewatia
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[gmx-users] Re: positive Leonard Jones Energy (Mark Abraham)

[Gideon Lapidoth]

Hi Mark,
Thanks for your answer. My ultimate goal is to compare biding affinities
between different ligands to the same protein using the LIE method. two
things bother though; First is the relatively high electrostatic  energy I
got between the ligand and the solvent which is considerably higher (about 5
times higher) than the electrostatic energy between the molecule and the
protein , therefore using the lie equation I got a positive delta G of
binding  which is obviously not correct (the LJ energy values cannot
compensate for the electrostatic energy difference). Secondly, my more
immediate concern is to understand why I would get a positive LJ value.

What do you think?

Thanks,
Gideon

> Hi all,
>
> I ran g_energy in order to calculate the LJ energy between a pip2
> (Phosphatidylinositol 4,5-bisphosphate) molecule and the
> solvent using GROMACS 4.0.7. the pip2  molecule is very polar and the
> avg. coulomb energy value I got between the ligand and solvent was ~
> 3100 KJ.

An equilibrated condensed-phase system of mixed positive and negative
charges using a normal biomolecular force field should have negative
Coulomb PE.

> The solvent includes water molecules and Cl and Na ions to counter the
> pip2 charge. the production run was done in npt conditions. the total
> charge of the pip2 molecule is -6 e. The avg. LJ  energy I got was
> ~190 KJ.
> I am trying make sense of this. could it be that the polar
> interactions between the solvent and ligand are so strong that they
> can influence a positive LJ energy?
> Does anyone have any idea why this could be ?

Force fields are parameterized to reproduce certain experimental or
computational results, in the hope that such reproduction will permit
simulations using that force field to sample similar chemical ensembles
with correct frequencies. They're not parameterized such that the
absolute values of any energies or energy components means anything, and
one has to work hard to demonstrate anything sensible about energy
differences, too. What were you hoping to observe?

Mark

-- 

Gideon Lapidoth,

MS.c candidate

Hemi Gutman Biophysics Lab

Department of Biochemistry & Molecular Biology

George S. Wise Faculty of Life Sciences

Tel Aviv University

Israel 69978



Tel: (972-3) 640-9824
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