Re: [gmx-users] calculation of self energy of protein

[Saumyak Mukherjee]

Thank you very much.

On 27 March 2017 at 02:22, Justin Lemkul  wrote:

>
>
> On 3/26/17 4:49 PM, Saumyak Mukherjee wrote:
>
>> Dear Justin,
>>
>> Thanks for the reply.
>>
>> I have tried that already. I stripped out the protein trajectory using
>> trjconv, created an appropriate .tpr file using tpbconv (I am using
>> GROMACS
>> 4.5.6), and recalculated energy using mdrun -rerun.
>>
>> But does the resulting .edr file include only the inherent energy of the
>> protein or does it have information of the interaction energies with the
>> solvent as well? That precisely is the point I am confused about.
>>
>> I tried this with a protein in water system and also simulated a dry
>> protein separately to compare. The energies were way to different from
>> each
>> other. Does it mean that the solvent-protein interaction energies are also
>> involved?
>>
>>
> If you have a protein-only trajectory and a protein-only .tpr file,
> there's no possible way for there to be any sort of protein-solvent
> interaction energy. The energies of a "wet" and "dry" protein system should
> be extremely different.
>
> -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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>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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[gmx-users] MMPBSA analysis on GROMACS trajectory

[Neha Gupta]

Hi gromacs users,

How to calculate MMPBSA analysis on Gromacs trajectory using MMPBSA tool of
amber software package?


Thanks,
Neha
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[gmx-users] Lipid water simulation

[Sheikh Imamul Hossain]

Hi all,

I am trying to simulate 1024 dppc lipids with water. I have prepared my
system using Charmm-Gui monolayer builder. Then I converted the atomistic
system to coarse grained system using bacdward.py. The box size I got in
the gro file was 18.246   18.38  23.7. Then I added CG water between the
two dppc monolayers within the box 18.246   18.384.22. The I increased
the box size to 18.246  18.3850.00. The total number of CG water is
6144. I minimized the system then equilibrated the system three times with
time steps 2fs, 10fs and 15fs. Then I did the production run for 2
microsecond using 20fs time steps. The temperature 310K was used in surface
tension coupling with surface tension 20mN/m per leaflet. I  have few
questions

1. After the first equilibration some (very few) CG water found in the air
space of the box  i.e in the top and bottom of the dppc monolayers. Which
are supposed to be attached together with other water between the two
monolayer. Is there any solution to prevent this?

2. Is there any other option to build the CG monolayer system and adding CG
water between the two monolayers? I used gmx solvate to add water.

3. I used 6 CG water per lipid. How many CG water can be added against the
number of lipids?

N.B.

After analyzing my system with the help of Bevan Lab DPPC tutorials I got
the area per lipid 0.5845. I used the formula
Area per lipid = (Box-X*Box-Y)/ # of lipid per leaflet

Thanks in advance.

Sincerely Your’s
Sheikh Imamul Hossain
PhD student at QUT
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[gmx-users] Using the md integrator for calculating free energy of solvation

[Dan Gil]

Hi,

I am following Dr. Sander Pronk's and Dr. Justin Lemkul's tutorial on
calculating free energy of solvation. Is it possible and theoretically
sound to use the md integrator instead of the sd integrator for these
calculations?

I have already done a considerable amount of work using md integration, and
I want to make sure that the free energy values I calculate are consistent
with my previous work.

If using the md integrator is not sound, is there an alternative way of
calculating solvation energy that will be consistent?

Best Regards,

Dan
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Re: [gmx-users] calculation of self energy of protein

[Justin Lemkul]

On 3/26/17 4:49 PM, Saumyak Mukherjee wrote:

Dear Justin,

Thanks for the reply.

I have tried that already. I stripped out the protein trajectory using
trjconv, created an appropriate .tpr file using tpbconv (I am using GROMACS
4.5.6), and recalculated energy using mdrun -rerun.

But does the resulting .edr file include only the inherent energy of the
protein or does it have information of the interaction energies with the
solvent as well? That precisely is the point I am confused about.

I tried this with a protein in water system and also simulated a dry
protein separately to compare. The energies were way to different from each
other. Does it mean that the solvent-protein interaction energies are also
involved?



If you have a protein-only trajectory and a protein-only .tpr file, there's no 
possible way for there to be any sort of protein-solvent interaction energy. 
The energies of a "wet" and "dry" protein system should be extremely different.


-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] calculation of self energy of protein

[Saumyak Mukherjee]

Dear Justin,

Thanks for the reply.

I have tried that already. I stripped out the protein trajectory using
trjconv, created an appropriate .tpr file using tpbconv (I am using GROMACS
4.5.6), and recalculated energy using mdrun -rerun.

But does the resulting .edr file include only the inherent energy of the
protein or does it have information of the interaction energies with the
solvent as well? That precisely is the point I am confused about.

I tried this with a protein in water system and also simulated a dry
protein separately to compare. The energies were way to different from each
other. Does it mean that the solvent-protein interaction energies are also
involved?

Thanks and regards,
Saumyak

On 26 March 2017 at 19:51, Justin Lemkul  wrote:

>
>
> On 3/26/17 10:06 AM, Saumyak Mukherjee wrote:
>
>> Yes, I need to calculate the inherent potential energy of the protein.
>>
>>
> You can strip the protein coordinates from the original trajectory, create
> a matching .tpr with convert-tpr and re-calculate energies with mdrun
> -rerun.  The quantity is a force field-dependent potential energy and is
> unlikely to be useful, though.
>
> -Justin
>
>
> On 26 March 2017 at 14:33, Souparno Adhikary 
>> wrote:
>>
>> Do you mean the potential energy of the protein?
>>>
>>> On 26 Mar 2017 14:24, "Saumyak Mukherjee" >> >
>>> wrote:
>>>
>>> Dear Users,

 How can the self energy of a protein be calculated from GROMACS. This

>>> means
>>>
 that I want only the inherent energy of the protein, excluding the
 interaction energy with the surrounding solvent.

 Adding to this, is it possible to calculate such inherent energy of any
 selected domain in the system, such as the hydration layer around

>>> protein?
>>>

 Thanks and regards,

 
 *Saumyak Mukherjee*

 Junior Research Fellow
 Prof. Biman Bagchi's Group
 Solid State and Structural Chemistry Unit
 Indian Institute of Science
 Bangalore - 560012

 Mob : 8017292426
 Alternative e-mail : saumyakmukher...@gmail.com
 smukher...@sscu.iisc.ernet.in
 
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>>>
>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
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>



-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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Re: [gmx-users] Replica exchange: exchanging pressures

[Justin Lemkul]

On 3/26/17 4:25 PM, Ramon Crehuet Simon wrote:

Dear all,
I'd like to run a replica exchange, but instead of exchanging temperatures, I 
would like to exchange pressures. I know this does not help enhance sampling, 
but I would like to create several ensembles at different pressures and I want 
them to mix, as RE does.
After preparing and equilibrating the system at each pressure, when I try to 
run RE, Gromacs complains that the systems are identical:

Fatal error:
The properties of the 8 systems are all the same, there is nothing to exchange
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

They are not, ref-p and compressibility are different in each md.mdp. Is there 
a way to tell Gromacs that it should exchange pressures? Or is this simply not 
implemented?


It's not implemented.

-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: exchanging pressures

[Ramon Crehuet Simon]

Dear all, 
I'd like to run a replica exchange, but instead of exchanging temperatures, I 
would like to exchange pressures. I know this does not help enhance sampling, 
but I would like to create several ensembles at different pressures and I want 
them to mix, as RE does. 
After preparing and equilibrating the system at each pressure, when I try to 
run RE, Gromacs complains that the systems are identical: 

Fatal error: 
The properties of the 8 systems are all the same, there is nothing to exchange 
For more information and tips for troubleshooting, please check the GROMACS 
website at http://www.gromacs.org/Documentation/Errors 

They are not, ref-p and compressibility are different in each md.mdp. Is there 
a way to tell Gromacs that it should exchange pressures? Or is this simply not 
implemented? 
Thanks in advance, 
Ramon 

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Re: [gmx-users] Protein preparation

[Justin Lemkul]

On 3/26/17 12:39 PM, Quin K wrote:

Thank you for the reply.

I have another question. I used MODELLER on Chimera to fix the protein and
found that there were significant visible changes to structure of protein.
I'm not sure whether to use the old protein or the fixed one.
Does it really matter that I used unfixed protein if the structure of
binding site(s) and important chain features remain the same ?
For the 50 ns MD simulation I never fixed the protein.



This all depends on what "fixed" means.  Were there missing residues?  Clashes 
in the structure?  In the case of the former, without a "fix" then the missing 
residues will cause lots of problems.  In the case of the latter, energy 
minimization is usually sufficient to alleviate any problems.


-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] Protein preparation

[Quin K]

Thank you for the reply.

I have another question. I used MODELLER on Chimera to fix the protein and
found that there were significant visible changes to structure of protein.
I'm not sure whether to use the old protein or the fixed one.
Does it really matter that I used unfixed protein if the structure of
binding site(s) and important chain features remain the same ?
For the 50 ns MD simulation I never fixed the protein.

Regards
Quin.

On Sun, Mar 26, 2017 at 7:51 PM, Justin Lemkul  wrote:

>
>
> On 3/26/17 9:44 AM, Quin K wrote:
>
>> Hi
>>
>> I'm new to Gromacs.
>> I have a question regarding protein preparation for MD simulation.
>>
>> I ran a 50 ns MD simulation but later found out that the protein has a
>> charge.
>> I found that there is a Mg2+ Ion in the protein crystal structure. Should
>> I
>> remove this Mg2+ ion from protein before addition of ions to the protein
>> ??
>>
>> Following is the protein I used.
>>
>> http://www.rcsb.org/pdb/explore.do?structureId=3a5j
>>
>>
> If the ion is catalytically or structurally significant it should be
> retained. If it's a consequence of some crystallization medium and may not
> be relevant in solution or for whatever your purposes are, then it can be
> removed.  But that's your homework to do based on your understanding of the
> biology and the goals of your work.
>
> -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] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

[Sajeewa Pemasinghe]

Thank you very much. I really appreciate your help.

On Sun, Mar 26, 2017 at 6:16 PM, Justin Lemkul  wrote:

>
>
> On 3/24/17 1:54 PM, Sajeewa Pemasinghe wrote:
>
>> Hi,
>>
>> I have two molecules which are not moving in the z axis due to being
>> continuous across the periodic boxes. I want to keep the distance between
>> them fixed by pulling along x and y axes. So as I am pulling along x and y
>> axes does my ncoords = 2 ?  By going along with this logic as long as my
>> pull-geometry = distance, will the maximum number for ncoords be 3 (i.e.
>> pulling along all x, y , and z axes)? I really appreciate an explanation.
>>
>>
> The "pull-ncoords" option tells grompp how many biasing potentials there
> are, not anything to do with which Cartesian directions are biased.
>
> -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] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

[Sajeewa Pemasinghe]

Thank you very much. I really appreciate it.

On Sun, Mar 26, 2017 at 6:17 PM, Justin Lemkul  wrote:

>
>
> On 3/26/17 8:11 AM, Sajeewa Pemasinghe wrote:
>
>> Hi all,
>>
>> I have a system in which I need to maintain the center of mass distance
>> between two molecules constant for an umbrella window. The structures are
>> not strictly aligned along an axis as they are the product of an
>> equilibrium simulation.I have the following code.
>>
>> pull = umbrella
>> pull_ngroups = 2
>> pull_group1_name = molecule1
>> pull_group2_name = molecule2
>> pull_coord1_type = umbrella
>> pull-geometry = distance
>> pull_coord1_groups = 1 2
>> pull-dim = Y N N
>> pull_coord1_rate = 0.0
>> pull_coord1_k = 2000
>>
>> I have the following questions.
>>
>> 1) Does pull-dim = Y N N mean that the k=2000 is applied along the x
>> coordinates only in maintaining the distance constant?
>>
>>
> Yes.
>
> 2) If I want to apply a harmonic potential to maintain the distance along
>> both x and y axis constant (in maintaining the distance *r* constant) do I
>> have to make the following changes?
>>
>> pull_coord2_groups = 1 2
>> pull-dim = Y Y N
>> pull_coord2_k = 2000  # this is applied on the y coordinate (that is the
>> picture I have in my mind)
>>
>>
> No.  You have one biasing potential that acts along x and y.  The biasing
> force is applied based on the distance calculated along those two axes, not
> independently in x and y.
>
> -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] Secondary structure analysis

[Souparno Adhikary]

I think dssp is a useful tool for this purpose...

Souparno

On 26 Mar 2017 19:50, "Justin Lemkul"  wrote:

>
>
> On 3/26/17 8:21 AM, RAHUL SURESH wrote:
>
>> I use gromacs 2016.1 version. How to do secondary structure analysis ?
>>
>>
> http://manual.gromacs.org/documentation/2016.1/user-guide/
> cmdline.html#protein-specific-analysis
>
> -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
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Re: [gmx-users] calculation of self energy of protein

[Justin Lemkul]

On 3/26/17 10:06 AM, Saumyak Mukherjee wrote:

Yes, I need to calculate the inherent potential energy of the protein.



You can strip the protein coordinates from the original trajectory, create a 
matching .tpr with convert-tpr and re-calculate energies with mdrun -rerun.  The 
quantity is a force field-dependent potential energy and is unlikely to be 
useful, though.


-Justin


On 26 March 2017 at 14:33, Souparno Adhikary  wrote:


Do you mean the potential energy of the protein?

On 26 Mar 2017 14:24, "Saumyak Mukherjee" 
wrote:


Dear Users,

How can the self energy of a protein be calculated from GROMACS. This

means

that I want only the inherent energy of the protein, excluding the
interaction energy with the surrounding solvent.

Adding to this, is it possible to calculate such inherent energy of any
selected domain in the system, such as the hydration layer around

protein?


Thanks and regards,


*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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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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Re: [gmx-users] Protein preparation

[Justin Lemkul]

On 3/26/17 9:44 AM, Quin K wrote:

Hi

I'm new to Gromacs.
I have a question regarding protein preparation for MD simulation.

I ran a 50 ns MD simulation but later found out that the protein has a
charge.
I found that there is a Mg2+ Ion in the protein crystal structure. Should I
remove this Mg2+ ion from protein before addition of ions to the protein ??

Following is the protein I used.

http://www.rcsb.org/pdb/explore.do?structureId=3a5j



If the ion is catalytically or structurally significant it should be retained. 
If it's a consequence of some crystallization medium and may not be relevant in 
solution or for whatever your purposes are, then it can be removed.  But that's 
your homework to do based on your understanding of the biology and the goals of 
your work.


-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
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Re: [gmx-users] Secondary structure analysis

[Justin Lemkul]

On 3/26/17 8:21 AM, RAHUL SURESH wrote:

I use gromacs 2016.1 version. How to do secondary structure analysis ?



http://manual.gromacs.org/documentation/2016.1/user-guide/cmdline.html#protein-specific-analysis

-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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Re: [gmx-users] Gromacs for polymer and biomolecule system

[Justin Lemkul]

On 3/26/17 8:46 AM, Riya Rogers wrote:

Dear All

I am new to Gromacs, I wanted to simulate Polymer system with biomolecule.

Is there any tutorial?

Also, how to include CNT with protein?

Any suggestions ?



In general, use pdb2gmx to generate the protein topology, then generate your 
polymer or CNT topology (the method depends on what these materials are, but 
either pdb2gmx if it's a linear polymer or x2top if it's a CNT) and #include it 
within a system .top of your own creation or within the protein .top from pdb2gmx.


There are CNT tutorials online, just use Google.

-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] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

[Justin Lemkul]

On 3/26/17 8:11 AM, Sajeewa Pemasinghe wrote:

Hi all,

I have a system in which I need to maintain the center of mass distance
between two molecules constant for an umbrella window. The structures are
not strictly aligned along an axis as they are the product of an
equilibrium simulation.I have the following code.

pull = umbrella
pull_ngroups = 2
pull_group1_name = molecule1
pull_group2_name = molecule2
pull_coord1_type = umbrella
pull-geometry = distance
pull_coord1_groups = 1 2
pull-dim = Y N N
pull_coord1_rate = 0.0
pull_coord1_k = 2000

I have the following questions.

1) Does pull-dim = Y N N mean that the k=2000 is applied along the x
coordinates only in maintaining the distance constant?



Yes.


2) If I want to apply a harmonic potential to maintain the distance along
both x and y axis constant (in maintaining the distance *r* constant) do I
have to make the following changes?

pull_coord2_groups = 1 2
pull-dim = Y Y N
pull_coord2_k = 2000  # this is applied on the y coordinate (that is the
picture I have in my mind)



No.  You have one biasing potential that acts along x and y.  The biasing force 
is applied based on the distance calculated along those two axes, not 
independently in x and y.


-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] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

[Justin Lemkul]

On 3/24/17 1:54 PM, Sajeewa Pemasinghe wrote:

Hi,

I have two molecules which are not moving in the z axis due to being
continuous across the periodic boxes. I want to keep the distance between
them fixed by pulling along x and y axes. So as I am pulling along x and y
axes does my ncoords = 2 ?  By going along with this logic as long as my
pull-geometry = distance, will the maximum number for ncoords be 3 (i.e.
pulling along all x, y , and z axes)? I really appreciate an explanation.



The "pull-ncoords" option tells grompp how many biasing potentials there are, 
not anything to do with which Cartesian directions are biased.


-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] Pull code grompp error

[Justin Lemkul]

On 3/24/17 11:18 AM, Souparno Adhikary wrote:

Hi Kausar,

I tried it with an index file. It seemed to run fine but did not produce
any "pull" i.e. shifting away of the DNA molecule from the protein. I used
a harmonic potential. And also, why do I need to specify the index file
when, according to the error itself, it can be run without making an index
file, just putting the name of the molecules?



GROMACS has certain default groups that include anything specified as a 
[moleculetype] name.  Anything else has to be formed as an index group.


-Justin


Thanks,

Souparno

On Fri, Mar 24, 2017 at 1:03 PM, Tasneem Kausar 
wrote:


Define you pull group in index file  as the error message says.

On Fri, Mar 24, 2017 at 12:18 PM, Souparno Adhikary  0

When I tried to grompp using this code, it generates an error:

Fatal error:
Group topol_Protein_chain_A referenced in the .mdp file was not found in
the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

I searched for the solutions in the Gromacs forum and found it might be

due

to name mismatch. But, in my case, the names are exactly same as

referenced

in the *.mdp file. Below is the molecule names from the topol.top file.

[ molecules ]
; Compound#mols
Protein_chain_A 1
DNA_chain_B 1
DNA_chain_C 1
SOL 33542
NA   125
CL   98

Can you please help to solve the problem? I tried with changing the names
to Protein and DNA (the residue types) and changing the ngroups to 3.
Nothing worked.

Regards,

Souparno Adhikary
University of Calcutta,
India.
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] Calculate area per head group

[Justin Lemkul]

On 3/23/17 3:50 PM, Poncho Arvayo Zatarain wrote:



Hello Gromacs users: I know there is not about Gromacs, but i want to calculate 
area per headgroup through simulation time. Anybody knos about a tutorial of 
GridMAT or can help me please? Thanks



We give examples in the Appendix of the user manual.  Please look through those 
and if you have questions contact me as this is not a GROMACS issue.


-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] gmx bar histogram data

[Justin Lemkul]

On 3/23/17 3:16 PM, Eric Smoll wrote:

Hello GROMACS users,

I am using the "gmx bar" tool in GROMACS 5.1.2 and am interested in
understanding the relevance of the histogram data output by the -oh flag.
Dr. Lemkul provides a very helpful reference

and a summary

which states:

"in order to obtain a reliable estimate of ΔG, we need adequate sampling
within each window (based on ∂H/∂λ distributions) and between neighboring
windows (ΔH distributions). The significant overlap in the distributions of
the data shown here and the low error estimate printed by gmx bar indicate
that we have achieved this goal. If your own calculations give you
non-overlapping histograms, resulting in large error estimates, then you
likely either need longer simulations, more λ states, or better parameters
for whatever molecule it is you are trying to transform."

When using the (default) mdp setting calc_lambda_neighbours=1, I assume
that the only overlap that matters is immediate-neighbour histogram
overlap. For example, when examining deltaH histograms that track the
"forward difference" lambda[i+1]-lambda[i], it only needs to show good
overlap with the lambda[i+2]-lambda[i+1] and lambda[i]-lambda[i-1]
histograms. Am I correct?



Yes.

-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] Regarding Glycine structure

[Justin Lemkul]

On 3/23/17 2:05 PM, Dilip H N wrote:

Hello,

I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and in
the first step if i do the energy minimization and then visualizes the
mixture, the glycine is no more in its pure form as before instead it has
been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
bonds with water are also broken. How can i solve these both issues..??



Glycine didn't convert between forms.  That's impossible; bonds can't break or 
form in a molecular mechanical process.  The termini are exactly what you 
assigned them to be.  If you want them to be something else, you have to assign 
them as such with pdb2gmx.  Though you should note that NH2 and COOH can't 
coincide at any real pH value.


-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] GPU computing for explicit solvation systems

[Justin Lemkul]

On 3/22/17 12:48 PM, mina solhtalab wrote:

Hi,I'd like to know if it is possible to use GPU computing for running simulations in GROMACS 
(version 5.1.4) while using an "explicit solvation system". I saw in the GROMACS website 
that the first attempts in GPU computing for GROMACS was only supporting "implicit solvation 
systems". So in new versions of GROMACS, is there any way to do aMDS by GPU computing when 
considering all atoms explicitly?


Yes, this has been supported natively for years.  The old limitation regarding 
implicit solvent was when OpenMM was required for GPU acceleration.  That hasn't 
been the case for a very long time.


-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] calculation of self energy of protein

[Saumyak Mukherjee]

Yes, I need to calculate the inherent potential energy of the protein.

On 26 March 2017 at 14:33, Souparno Adhikary  wrote:

> Do you mean the potential energy of the protein?
>
> On 26 Mar 2017 14:24, "Saumyak Mukherjee" 
> wrote:
>
> > Dear Users,
> >
> > How can the self energy of a protein be calculated from GROMACS. This
> means
> > that I want only the inherent energy of the protein, excluding the
> > interaction energy with the surrounding solvent.
> >
> > Adding to this, is it possible to calculate such inherent energy of any
> > selected domain in the system, such as the hydration layer around
> protein?
> >
> > Thanks and regards,
> >
> > 
> > *Saumyak Mukherjee*
> >
> > Junior Research Fellow
> > Prof. Biman Bagchi's Group
> > Solid State and Structural Chemistry Unit
> > Indian Institute of Science
> > Bangalore - 560012
> >
> > Mob : 8017292426
> > Alternative e-mail : saumyakmukher...@gmail.com
> > smukher...@sscu.iisc.ernet.in
> > 
> > --
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-- 

*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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[gmx-users] Protein preparation

[Quin K]

Hi

I'm new to Gromacs.
I have a question regarding protein preparation for MD simulation.

I ran a 50 ns MD simulation but later found out that the protein has a
charge.
I found that there is a Mg2+ Ion in the protein crystal structure. Should I
remove this Mg2+ ion from protein before addition of ions to the protein ??

Following is the protein I used.

http://www.rcsb.org/pdb/explore.do?structureId=3a5j

Thanks
Regards!
Quin.
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[gmx-users] Gromacs for polymer and biomolecule system

[Riya Rogers]

Dear All

I am new to Gromacs, I wanted to simulate Polymer system with biomolecule.

Is there any tutorial?

Also, how to include CNT with protein?

Any suggestions ?


Regards
Riya
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[gmx-users] Gromacs for polymer and biomolecule system

[Riya Rogers]

Dear All

I am new to Gromacs, I wanted to simulate Polymer system with biomolecule.

Is there any tutorial?

Also, how to include CNT with protein?

Any suggestions ?


Regards
Riya
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[gmx-users] Secondary structure analysis

[RAHUL SURESH]

I use gromacs 2016.1 version. How to do secondary structure analysis ?

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] Need for a clarification between "umbrella restraints" and value for "ncoords" in GROMACS pull code

[Sajeewa Pemasinghe]

Hi all,

I have a system in which I need to maintain the center of mass distance
between two molecules constant for an umbrella window. The structures are
not strictly aligned along an axis as they are the product of an
equilibrium simulation.I have the following code.

pull = umbrella
pull_ngroups = 2
pull_group1_name = molecule1
pull_group2_name = molecule2
pull_coord1_type = umbrella
pull-geometry = distance
pull_coord1_groups = 1 2
pull-dim = Y N N
pull_coord1_rate = 0.0
pull_coord1_k = 2000

I have the following questions.

1) Does pull-dim = Y N N mean that the k=2000 is applied along the x
coordinates only in maintaining the distance constant?

2) If I want to apply a harmonic potential to maintain the distance along
both x and y axis constant (in maintaining the distance *r* constant) do I
have to make the following changes?

pull_coord2_groups = 1 2
pull-dim = Y Y N
pull_coord2_k = 2000  # this is applied on the y coordinate (that is the
picture I have in my mind)

I am really confused here. I really appreciate some help with this.

Thank you very much

Sajeewa
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Re: [gmx-users] calculation of self energy of protein

[Souparno Adhikary]

Do you mean the potential energy of the protein?

On 26 Mar 2017 14:24, "Saumyak Mukherjee" 
wrote:

> Dear Users,
>
> How can the self energy of a protein be calculated from GROMACS. This means
> that I want only the inherent energy of the protein, excluding the
> interaction energy with the surrounding solvent.
>
> Adding to this, is it possible to calculate such inherent energy of any
> selected domain in the system, such as the hydration layer around protein?
>
> Thanks and regards,
>
> 
> *Saumyak Mukherjee*
>
> Junior Research Fellow
> Prof. Biman Bagchi's Group
> Solid State and Structural Chemistry Unit
> Indian Institute of Science
> Bangalore - 560012
>
> Mob : 8017292426
> Alternative e-mail : saumyakmukher...@gmail.com
> smukher...@sscu.iisc.ernet.in
> 
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[gmx-users] calculation of self energy of protein

[Saumyak Mukherjee]

Dear Users,

How can the self energy of a protein be calculated from GROMACS. This means
that I want only the inherent energy of the protein, excluding the
interaction energy with the surrounding solvent.

Adding to this, is it possible to calculate such inherent energy of any
selected domain in the system, such as the hydration layer around protein?

Thanks and regards,


*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukher...@gmail.com
smukher...@sscu.iisc.ernet.in

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