[gmx-users] g_lie and ligand only simulation

[Kavyashree M]

Dear Users,

Its mentioned in the list that it would be
wrong to use g_lie on a simulation which
uses PME.

So kindly suggest any other way available
to get the free energy of ligand binding other
using g_lie?

Thank you
Regards
kavya
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[gmx-users] g_lie and ligand only simulation

[Kavyashree M]

Dear Gromacs users,

I have a protein-ligand in water simulation (Gmx 4.5.3), for
calculating free energy of ligand binding, a separate simulation
of ligand in water simulation is required (which I read from the
list). The question is the protein-ligand is simulated as a dimeric
system so is it necessary to simulate the ligand in water as
a dimer too.

Please clarify.

Thank you
Regards
Kavya
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[gmx-users] Re: Hardware for best gromacs performance?

[jonyer]

Have you used/considered any cloud approaches?

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[gmx-users] ligand problem

[kiana moghaddam]

Hi gmx-users
I prepared the DNA topology by using the parmbsc0 force field. I want to apply 
the GAFF force field for the ligand by using the antechamber module of 
ambertools13.
I optimized my ligand by Gaussian program at B3lyp/6-31G* in solvent (water) 
phase, but I don't know how to calculate RESP for the ligand by antechamber.
can someone help me to address this problem?
Best Regards 
kiana
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[gmx-users] Re: Hardware for best gromacs performance?

[Brad Van Oosten]

Im not sure on the prices of these systems any more, they are getting dated
so they will be on the low end price wise. I have a 30,000 ish atom lipid
system for all my simulations so this might be helpful:

System 1
CPU - dual 6 core xeon @ 2.8 GHz
GPU - 2x GTX 680
50 ns/day

System 2
CPU - dual 4 core intel E5607 @ 2.26 GHz
GPU - 2x M2070
45 ns/day

System 3
CPU - dual 4 core intel E5620 @ 2.40 GHz
GPU - 1x GTX 680
40 ns/day



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[gmx-users] Gibbs Energy Calculation and charges

[Christopher Neale]

Dear Dallas:

Seems like you could test Michael's idea by removing all 1-4 NB interactions 
from your topology. It won't produce any biologically useful results, but might 
be a worthwhile check to see if indeed this is the issue.

To do this, I figure you would set gen-pairs to "no" in the [ defaults ] 
directive of forcefield.itp, remove the [ pairtypes ] section from 
ffnonbonded.itp, and remove the [ pairs ] section from your molecular .itp 
file. (You can quickly check that the 1-4 energy is zero in all states to 
ensure that this works).

If that gives you the result that you expect, then you could go on to 
explicitely state the 1-4 interactions for the A and B states (I presume that 
this is possible). Of course, you should be able to jump directly to this 
second test, but the first test might be useful because it rules out the 
possibility that you make a typo somewhere.

Chris.

-- original message --

I think the grammar got a little garbled there, so I'm not sure quite
what you are claiming.

One important thing to remember; 1-4 interactions are treated as
bonded interactions right now FOR COUPLE intramol (not for lambda
dependence of the potential energy function), so whether
couple-intramol is set to yes or no does not affect these interactions
at all.  It only affects the nonbondeds with distances greater than
1-5.  At least to me, this is nonintuitive (and we're coming up with a
better scheme for 5.0), but might that explain what you are getting?

On Tue, Oct 29, 2013 at 9:44 PM, Dallas Warren  
wrote:
> Just want this to make another pass, just in case those in the know missed it.
>
> Using couple-intrmol = yes the resulting dH/dl plot actually looks like that 
> at lamba = 1 it is actually equal to couple-intramol = no with lambda = 0.
>
> Should that be the case?
>
> Catch ya,
>
> Dr. Dallas Warren
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Re:Re: [gmx-users] ligand-protein simulation

[xiao]

Hi Justin,
 
Thank you very much for your response.
I used GAFF force field parameters for the ligand. I have done another short MD 
simulation, and this time everything seems fine, so i have no idea where the 
problem is from.
 
Best wishes
Fugui




At 2013-11-01 20:41:46,"Justin Lemkul"  wrote:
>
>
>On 11/1/13 5:37 AM, xiao wrote:
>> Dear all gromacs users,
>>
>> I have run a protein-ligand simulations. However, the position of the ligand
>> is not reasonable after 10ns simulation. There is no problem with the force
>> field paramers of the ligand. I am trying to constrict the ligand move for
>> 500ps simulation. But i do not know whether it will work. Any good idea is
>> appreciated :)
>>
>
>Usually when something misbehaves, the topology is the first likely source of 
>error.  How have you concluded that it is suitable?
>
>Since we don't know what you're doing (description of your protocol, or even 
>better, .mdp files), it could simply be that you're doing something that 
>causes 
>the physical model to be wrong.  Provide that information and you're more 
>likely 
>to get a quick and productive response.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 601
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
>==
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Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

[jkrieger]

I notice that both papers mention modifications to GROMACS and cite the
following:
http://www.ncbi.nlm.nih.gov/pubmed/16471903

> Following up on Justin's reply I just want to add that, not only is it
> possible, as it has been done before. For instance:
>
> http://www.ncbi.nlm.nih.gov/pubmed/18214978
> http://www.ncbi.nlm.nih.gov/pubmed/22072522
>
> Luís Filipe
> ITQB-UNL, Portugal
>
> 2013/11/1 Justin Lemkul 
>
>>
>>
>> On 11/1/13 8:39 AM, xiao wrote:
>>
>>> It is impossible. But you can add proton to the acidic amino acid.
>>>
>>>
>> It's certainly not impossible.  There are constant-pH methods that
>> exist;
>> the list archive contains many posts on this topic, and more information
>> can be found at:
>>
>> http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation
>>
>> Whether or not you can easily accomplish such simulations in Gromacs is
>> another matter.
>>
>> Standard MD does not allow for dynamic protonation states, so the
>> closest
>> you can get without running more advanced MD is to use fixed protonation
>> states, assigned by pdb2gmx, that are indicative of the most prevalent
>> state of the residues at a given pH value.
>>
>> Changing ionic strength is trivial; that's what genion -conc is for.
>>
>> -Justin
>>
>>
>>
>>>
>>>
>>>
>>> At 2013-11-01 20:36:41,Mass  wrote:
>>>
 Dear Gromacs users,
 Just was wondering if it is possible to protein solution let say
 Lysozyme in Water example of Justin tutorial at different pH and ionic
 strengths, if so how?
 Thanks
 --
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>> --
>> ==**
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.**edu 
>> | (410)
>> 706-7441
>>
>> ==**
>>
>> --
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Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

[Luís Carlos Filipe]

Following up on Justin's reply I just want to add that, not only is it
possible, as it has been done before. For instance:

http://www.ncbi.nlm.nih.gov/pubmed/18214978
http://www.ncbi.nlm.nih.gov/pubmed/22072522

Luís Filipe
ITQB-UNL, Portugal

2013/11/1 Justin Lemkul 

>
>
> On 11/1/13 8:39 AM, xiao wrote:
>
>> It is impossible. But you can add proton to the acidic amino acid.
>>
>>
> It's certainly not impossible.  There are constant-pH methods that exist;
> the list archive contains many posts on this topic, and more information
> can be found at:
>
> http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation
>
> Whether or not you can easily accomplish such simulations in Gromacs is
> another matter.
>
> Standard MD does not allow for dynamic protonation states, so the closest
> you can get without running more advanced MD is to use fixed protonation
> states, assigned by pdb2gmx, that are indicative of the most prevalent
> state of the residues at a given pH value.
>
> Changing ionic strength is trivial; that's what genion -conc is for.
>
> -Justin
>
>
>
>>
>>
>>
>> At 2013-11-01 20:36:41,Mass  wrote:
>>
>>> Dear Gromacs users,
>>> Just was wondering if it is possible to protein solution let say
>>> Lysozyme in Water example of Justin tutorial at different pH and ionic
>>> strengths, if so how?
>>> Thanks
>>> --
>>> 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/Searchbefore
>>>  posting!
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>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read 
>>> http://www.gromacs.org/**Support/Mailing_Lists
>>>
>>>
>>>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
>
> --
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Re: [gmx-users] Lysozyme in Water at different pH and Ionic strength

[Justin Lemkul]

On 11/1/13 8:39 AM, xiao wrote:

It is impossible. But you can add proton to the acidic amino acid.



It's certainly not impossible.  There are constant-pH methods that exist; the 
list archive contains many posts on this topic, and more information can be 
found at:


http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

Whether or not you can easily accomplish such simulations in Gromacs is another 
matter.


Standard MD does not allow for dynamic protonation states, so the closest you 
can get without running more advanced MD is to use fixed protonation states, 
assigned by pdb2gmx, that are indicative of the most prevalent state of the 
residues at a given pH value.


Changing ionic strength is trivial; that's what genion -conc is for.

-Justin






At 2013-11-01 20:36:41,Mass  wrote:

Dear Gromacs users,
Just was wondering if it is possible to protein solution let say Lysozyme in 
Water example of Justin tutorial at different pH and ionic strengths, if so how?
Thanks
--
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] ligand-protein simulation

[Justin Lemkul]

On 11/1/13 5:37 AM, xiao wrote:

Dear all gromacs users,

I have run a protein-ligand simulations. However, the position of the ligand
is not reasonable after 10ns simulation. There is no problem with the force
field paramers of the ligand. I am trying to constrict the ligand move for
500ps simulation. But i do not know whether it will work. Any good idea is
appreciated :)



Usually when something misbehaves, the topology is the first likely source of 
error.  How have you concluded that it is suitable?


Since we don't know what you're doing (description of your protocol, or even 
better, .mdp files), it could simply be that you're doing something that causes 
the physical model to be wrong.  Provide that information and you're more likely 
to get a quick and productive response.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re:[gmx-users] Lysozyme in Water at different pH and Ionic strength

[xiao]

It is impossible. But you can add proton to the acidic amino acid.





At 2013-11-01 20:36:41,Mass  wrote:
>Dear Gromacs users,
>Just was wondering if it is possible to protein solution let say Lysozyme in 
>Water example of Justin tutorial at different pH and ionic strengths, if so 
>how?
>Thanks
>-- 
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[gmx-users] Lysozyme in Water at different pH and Ionic strength

[Mass]

Dear Gromacs users,
Just was wondering if it is possible to protein solution let say Lysozyme in 
Water example of Justin tutorial at different pH and ionic strengths, if so how?
Thanks
-- 
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[gmx-users] ligand-protein simulation

[xiao]

Dear all gromacs users,
 
I have run a protein-ligand simulations. However, the position of the ligand is 
not reasonable after 10ns simulation. There is no problem with the force field 
paramers of the ligand. I am trying to constrict the ligand move for 500ps 
simulation. But i do not know whether it will work. Any good idea is 
appreciated :)
 
Best wishes
 
Fugui-- 
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Re: [gmx-users] GMX manually generate topology for residues

[Mark Abraham]

They're http://en.wikipedia.org/wiki/C_preprocessor symbols that are
#defined elsewhere in the directory that contains that .rtp file. The
names/symbols probably map to the original force field literature. grep is
your friend.

Mark


On Fri, Nov 1, 2013 at 6:45 AM, charles  wrote:

> i am a newbie to gromacs, trying to generate a new rtp entry for my
> residue.
> Bonds, dihedrals of .rtp file has gb_XX
> what is gb_XX numbers? how can get informations about that?
> How to define those velues for my residues?
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Re: [gmx-users] probability distribution of bond distance/length

[Mark Abraham]

On Fri, Nov 1, 2013 at 4:04 AM, Xu Dong Huang  wrote:

> Dear all,
>
> I would like to assess the probability distribution of particle bond
> distance/length over the entire run, specifically I want to collect
> possibly a histogram representation or even a regular plot. Would using
> g_bond be the correct way to obtain the probability distribution?


g_bond -h and/or manual chapter 8 are the best places to start.


> Or is there another function that gets probability distribution
> specifically. Also, if using g_bond, it will give me an average (I
> suppose), so how can I get a histogram/data series representation? (I do
> not want to visualize this result using xmgrace)
>

g_analyze, or your favourite maths/stats software package.

P.S I believe someone earlier suggested a link to the data collection
> reporting procedure, I tried it and changed the .xvg to a .csv, but the
> data reported in excel format all belongs to 1 single column, which won’t
> let me make a plot.
>

A plot of two columns, no, but it should let you plot a histogram!

Mark
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