Re: [gmx-users] DNA simulation and choice of temperature coupling groups

[Dallas Warren]

http://dx.doi.org/10.1021/ct8000365

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Wed, 29 Aug 2018 at 21:38, Athina Meletiou
 wrote:
>
> Hello all,
>
> I was looking into performing some MD simulations of a DNA molecule - as a 
> control to simulations of the same DNA molecule along with its binding 
> protein. However I’m getting a bit confused about how to use temperature 
> coupling groups. I am torn between simply using one group (“System”) or two 
> groups (“DNA” and “Water_and_ions”). I’m leaning towards a single group 
> (“System”) and that’s because 1) the groups I have used for the DNA and 
> binding protein simulations were “Protein” and “Non-protein”, meaning that in 
> those my DNA molecule was grouped together with the solvent and ions. 
> Therefore for comparability I’m thinking that using “System” for the DNA 
> simulations may be best. Also 2) using one group for the solute (DNA) and 
> another for the solvent (Water_and_ions) can introduce artifacts into the 
> conformational dynamics of my DNA molecule.
>
> I would appreciate any insights/hints, thank you all in advance.
>
> Kind regards,
> Athina
>
>
>
>
> This message and any attachment are intended solely for the addressee
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Re: [gmx-users] [BULK][EXT] Re: PDB code

[Justin Lemkul]

On 8/29/18 2:34 PM, Nick Johans wrote:

Thank you dear justin. I'll read the paper. But  practically it is
mentioned that (for simulation) it has 51 residues which exactly equal to
A,B chain.
And i hope you answer the question about protonating " Residues B23-B30
were
  removed from insulin 43 residues. The C-terminal carboxyl groups and all
  the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
  Parameterized force field parameters for
  protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
I didn't protonate the molecule, so when i used grompp, my system had not
integer charges, is it because of i ignore the polar groups and didn't
protonate carboxyl groups?


No, the quoted passage means all amino acids were treated in their 
conjugate acid form (i.e. the dominant form at extremely low pH). This 
has nothing to do with a non-integer charge, simply that if you did not 
do the same thing, you're going to get protonation according to the 
dominant form at neutral pH. If you don't have an integer, you have a 
problem that pdb2gmx should have warned you about (long bonds => missing 
atoms, etc.)


-Justin


Best
On Wed, 29 Aug 2018, 22:46 Justin Lemkul,  wrote:



On 8/29/18 2:13 PM, Nick Johans wrote:

Thank you so much Iris.
   want to simulate a protwin interaction with nanotube. The question is

the

pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin

has

4 chain?


You need to read the paper associated with that crystal structure as
well as header information in the PDB file as to why this is. A crystal
complex is not necessarily the same as a functional complex.

-Justin


On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:


Hi Nick,

I think the big question is what are you trying to simulate – what is

your

goal? It is critical that you now your protein (e.g. how was it
crystalized, any missing atoms, missing residues, hetero atoms,

ligands). I

think prior to building your system you should first understand your

goal

and get a stronger foundation on MDS as well as the forcefiled you

require

to model your system, this will help you better understand the flags for
each gmx command.

I would start with first reading the gromacs manual and re-reading the
reference paper associated with your PDB. Present your hypothesis and
goal(s) to your colleagues – this will help you formulate a
hypothesis-driven project.

Iris





[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1833992660]

Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH

44195  |

(216) 445-7885




From:  on behalf of
Nick Johans 
Reply-To: "gmx-us...@gromacs.org" 
Date: Wednesday, August 29, 2018 at 11:36 AM
To: "gmx-us...@gromacs.org" 
Subject: [BULK][EXT] Re: [gmx-users] PDB code

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp,

the

system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work

with

-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."


And how should protonate molecule in AMBER ff?

What does it mean "protonated" ? How they add H when they have used AMBER

forcefield?
Would you please help me?

Best regards
On Wed, 29 Aug 2018, 19:50 Nick Johans, 

wrote:

Hi,

I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology

file

of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When

you

google it, it is mentioned that insuline has 2 chains named A,B. So why
it's pdb code has 4 chains? Are they couple of each other? If yes and i
should remove C,D chains, is there any tool to remove them standardly
;)(not manually)?

How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
starting simulation?


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Re: [gmx-users] [BULK][EXT] Re: PDB code

[Nick Johans]

Thank you dear justin. I'll read the paper. But  practically it is
mentioned that (for simulation) it has 51 residues which exactly equal to
A,B chain.
And i hope you answer the question about protonating " Residues B23-B30
were
 removed from insulin 43 residues. The C-terminal carboxyl groups and all
 the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
 Parameterized force field parameters for
 protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
I didn't protonate the molecule, so when i used grompp, my system had not
integer charges, is it because of i ignore the polar groups and didn't
protonate carboxyl groups?

Best
On Wed, 29 Aug 2018, 22:46 Justin Lemkul,  wrote:

>
>
> On 8/29/18 2:13 PM, Nick Johans wrote:
> > Thank you so much Iris.
> >   want to simulate a protwin interaction with nanotube. The question is
> the
> > pdb file structure. As i have not simulate protein before and i know that
> > insulin has 2 chains the question is that why in pdbcode(3e7y) insulin
> has
> > 4 chain?
> >
>
> You need to read the paper associated with that crystal structure as
> well as header information in the PDB file as to why this is. A crystal
> complex is not necessarily the same as a functional complex.
>
> -Justin
>
> > On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:
> >
> >> Hi Nick,
> >>
> >> I think the big question is what are you trying to simulate – what is
> your
> >> goal? It is critical that you now your protein (e.g. how was it
> >> crystalized, any missing atoms, missing residues, hetero atoms,
> ligands). I
> >> think prior to building your system you should first understand your
> goal
> >> and get a stronger foundation on MDS as well as the forcefiled you
> require
> >> to model your system, this will help you better understand the flags for
> >> each gmx command.
> >>
> >> I would start with first reading the gromacs manual and re-reading the
> >> reference paper associated with your PDB. Present your hypothesis and
> >> goal(s) to your colleagues – this will help you formulate a
> >> hypothesis-driven project.
> >>
> >> Iris
> >>
> >>
> >>
> >>
> [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1833992660]
> >>
> >> Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
> >> Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH
> 44195  |
> >> (216) 445-7885
> >>
> >>
> >>
> >>
> >> From:  on behalf of
> >> Nick Johans 
> >> Reply-To: "gmx-us...@gromacs.org" 
> >> Date: Wednesday, August 29, 2018 at 11:36 AM
> >> To: "gmx-us...@gromacs.org" 
> >> Subject: [BULK][EXT] Re: [gmx-users] PDB code
> >>
> >> Sorry, i have just removed C,D chains by pymol and then started
> >> simulating(without adding any terminal or H,...)... but after grompp,
> the
> >> system had charges and were not integer. Is it because of i didn't add
> >> terminals? I use AMBER99SB forcefield and as you know it doesn't work
> with
> >> -ter but i have read paper which is said( that's my reference paper);
> >> " Residues B23-B30 were
> >> removed from insulin 43 residues. The C-terminal carboxyl groups and all
> >> the charged residues were set to be
> >> protonated to simulate the protein structures under acidic conditions.
> >> Parameterized force field parameters for
> >> protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
> >>
> > And how should protonate molecule in AMBER ff?
> >
> > What does it mean "protonated" ? How they add H when they have used AMBER
> >> forcefield?
> >> Would you please help me?
> >>
> >> Best regards
> >> On Wed, 29 Aug 2018, 19:50 Nick Johans, 
> wrote:
> >>
> >>> Hi,
> >>>
> >>> I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology
> file
> >>> of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When
> >> you
> >>> google it, it is mentioned that insuline has 2 chains named A,B. So why
> >>> it's pdb code has 4 chains? Are they couple of each other? If yes and i
> >>> should remove C,D chains, is there any tool to remove them standardly
> >>> ;)(not manually)?
> >>>
> >>> How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
> >>> starting simulation?
> >>>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List<
> >>
> https://protect-us.mimecast.com/s/TLbLCG6xpNtGGMziQt_Dy?domain=gromacs.org
> >
> >> before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<
> >>
> https://protect-us.mimecast.com/s/-YXNCJ6Avkt55YjUvCgAi?domain=gromacs.org
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users<
> >>
> https://protect-us.mimecast.com/s/HUA1CKrBwlimmnRSGaanT?domain=maillist.sys.kth.se
> >
> >> or send a mail to gmx-users-requ...@gromacs.org.
> >>
> >>
> >> ===
> >>
> >>
> 

Re: [gmx-users] [BULK][EXT] Re: PDB code

[Justin Lemkul]

On 8/29/18 2:13 PM, Nick Johans wrote:

Thank you so much Iris.
  want to simulate a protwin interaction with nanotube. The question is the
pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has
4 chain?



You need to read the paper associated with that crystal structure as 
well as header information in the PDB file as to why this is. A crystal 
complex is not necessarily the same as a functional complex.


-Justin


On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:


Hi Nick,

I think the big question is what are you trying to simulate – what is your
goal? It is critical that you now your protein (e.g. how was it
crystalized, any missing atoms, missing residues, hetero atoms, ligands). I
think prior to building your system you should first understand your goal
and get a stronger foundation on MDS as well as the forcefiled you require
to model your system, this will help you better understand the flags for
each gmx command.

I would start with first reading the gromacs manual and re-reading the
reference paper associated with your PDB. Present your hypothesis and
goal(s) to your colleagues – this will help you formulate a
hypothesis-driven project.

Iris



[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1833992660]

Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  |
(216) 445-7885




From:  on behalf of
Nick Johans 
Reply-To: "gmx-us...@gromacs.org" 
Date: Wednesday, August 29, 2018 at 11:36 AM
To: "gmx-us...@gromacs.org" 
Subject: [BULK][EXT] Re: [gmx-users] PDB code

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp, the
system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work with
-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."


And how should protonate molecule in AMBER ff?

What does it mean "protonated" ? How they add H when they have used AMBER

forcefield?
Would you please help me?

Best regards
On Wed, 29 Aug 2018, 19:50 Nick Johans,  wrote:


Hi,

I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file
of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When

you

google it, it is mentioned that insuline has 2 chains named A,B. So why
it's pdb code has 4 chains? Are they couple of each other? If yes and i
should remove C,D chains, is there any tool to remove them standardly
;)(not manually)?

How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
starting simulation?


--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List<
https://protect-us.mimecast.com/s/TLbLCG6xpNtGGMziQt_Dy?domain=gromacs.org>
before posting!

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or send a mail to gmx-users-requ...@gromacs.org.


===


  Please consider the environment before printing this e-mail

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Re: [gmx-users] [BULK][EXT] Re: PDB code

[Nick Johans]

Thank you so much Iris.
 want to simulate a protwin interaction with nanotube. The question is the
pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has
4 chain?


On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:

> Hi Nick,
>
> I think the big question is what are you trying to simulate – what is your
> goal? It is critical that you now your protein (e.g. how was it
> crystalized, any missing atoms, missing residues, hetero atoms, ligands). I
> think prior to building your system you should first understand your goal
> and get a stronger foundation on MDS as well as the forcefiled you require
> to model your system, this will help you better understand the flags for
> each gmx command.
>
> I would start with first reading the gromacs manual and re-reading the
> reference paper associated with your PDB. Present your hypothesis and
> goal(s) to your colleagues – this will help you formulate a
> hypothesis-driven project.
>
> Iris
>
>
>
> [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1833992660]
>
> Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
> Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  |
> (216) 445-7885
>
>
>
>
> From:  on behalf of
> Nick Johans 
> Reply-To: "gmx-us...@gromacs.org" 
> Date: Wednesday, August 29, 2018 at 11:36 AM
> To: "gmx-us...@gromacs.org" 
> Subject: [BULK][EXT] Re: [gmx-users] PDB code
>
> Sorry, i have just removed C,D chains by pymol and then started
> simulating(without adding any terminal or H,...)... but after grompp, the
> system had charges and were not integer. Is it because of i didn't add
> terminals? I use AMBER99SB forcefield and as you know it doesn't work with
> -ter but i have read paper which is said( that's my reference paper);
> " Residues B23-B30 were
> removed from insulin 43 residues. The C-terminal carboxyl groups and all
> the charged residues were set to be
> protonated to simulate the protein structures under acidic conditions.
> Parameterized force field parameters for
> protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
>
And how should protonate molecule in AMBER ff?

What does it mean "protonated" ? How they add H when they have used AMBER
> forcefield?
> Would you please help me?
>
> Best regards
> On Wed, 29 Aug 2018, 19:50 Nick Johans,  wrote:
>
> > Hi,
> >
> > I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file
> > of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When
> you
> > google it, it is mentioned that insuline has 2 chains named A,B. So why
> > it's pdb code has 4 chains? Are they couple of each other? If yes and i
> > should remove C,D chains, is there any tool to remove them standardly
> > ;)(not manually)?
> >
> > How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
> > starting simulation?
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List<
> https://protect-us.mimecast.com/s/TLbLCG6xpNtGGMziQt_Dy?domain=gromacs.org>
> before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<
> https://protect-us.mimecast.com/s/-YXNCJ6Avkt55YjUvCgAi?domain=gromacs.org
> >
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users<
> https://protect-us.mimecast.com/s/HUA1CKrBwlimmnRSGaanT?domain=maillist.sys.kth.se>
> or send a mail to gmx-users-requ...@gromacs.org.
>
>
> ===
>
>
>  Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
> you have received this communication in error, please contact the sender
> immediately and destroy the material in its entirety, whether electronic or
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Re: [gmx-users] Heterogeneous GPU cluster question?

[Szilárd Páll]

Hi,

You can use multiple types of GPUs in a single run, but it won't be ideal.
Also, with Volta GPUs you'll probably be better off also offloading PME
which won't scale to more than 2-3 GPUs, so probably you'll not want to use
more than 2 GPUs in run with Volta.

--
Szilárd


On Tue, Aug 28, 2018 at 4:31 PM Smith, Micholas D.  wrote:

> Dear users (and developers),
>
> My sys. admin. is exploring purchasing some more GPU nodes for our cluster
> and was curious if we could get away with running GROMACS on a cluster that
> has two different types of GPUs, i.e. 70% of the nodes have 2 p100 gpus
> while 30% have volta (both have 2 gpu's per node).?
>
> I've been looking through the mailing list, but haven't bumped into this
> situation before.
>
> My inclination was to just purchase the "older" p100 since that is what
> all of the nodes are currently sporting, but thought I would ask to see if
> anyone has tried this kind of set-up before.
>
> Thanks,
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD. MRSC
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: Tuesday, August 28, 2018 10:08 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] rerun doesn't calculate Coulomb & LJ interactions
> between groups
>
> On 8/28/18 10:04 AM, Irem Altan wrote:
> > Hi,
> >
> > I ran some umbrella sampling simulations on GPUs. I want to get the
> Coulomb and LJ energy between certain groups (chain A - chain B, chain A -
> solvent, etc.) , so I ran rerun:
> > gmx mdrun -rerun umbrella1.xtc -nb cpu -v -deffnm umbrella1
> > However, when I run gmx energy on the output .edr file:
> > gmx energy -f umbrella1.edr -o umbrella1_ener.xvg
> > I only get 50 terms listed, as opposed to ~90 that contains things like
> "LJ-SR:SOL-Chain_A". What am I missing?
> > The executable is created with the following command:
> > gmx grompp -f umbrella.mdp -c conf1.gro -p topol.top -n index.ndx
> -maxwarn 1 -o umbrella1.tpr
> > where chain A, chain B, and SOL are defined in index.ndx.
>
> The contents of index.ndx are irrelevant unless you've actually specific
> which energygrps you want to define (in the .mdp file). Also, why are
> you using -maxwarn 1? This should almost never be done.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] [BULK][EXT] Re: PDB code

[Smith, Iris]

Hi Nick,

I think the big question is what are you trying to simulate – what is your 
goal? It is critical that you now your protein (e.g. how was it crystalized, 
any missing atoms, missing residues, hetero atoms, ligands). I think prior to 
building your system you should first understand your goal and get a stronger 
foundation on MDS as well as the forcefiled you require to model your system, 
this will help you better understand the flags for each gmx command.

I would start with first reading the gromacs manual and re-reading the 
reference paper associated with your PDB. Present your hypothesis and goal(s) 
to your colleagues – this will help you formulate a hypothesis-driven project.

Iris


[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_1833992660]

Iris Nira Smith  |  Postdoctoral Fellow |  Genomic Medicine Institute
Cleveland Clinic  |  9500 Euclid Ave. / NE5-255  |  Cleveland, OH 44195  | 
(216) 445-7885




From:  on behalf of Nick 
Johans 
Reply-To: "gmx-us...@gromacs.org" 
Date: Wednesday, August 29, 2018 at 11:36 AM
To: "gmx-us...@gromacs.org" 
Subject: [BULK][EXT] Re: [gmx-users] PDB code

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp, the
system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work with
-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
What does it mean "protonated" ? How they add H when they have used AMBER
forcefield?
Would you please help me?

Best regards
On Wed, 29 Aug 2018, 19:50 Nick Johans,  wrote:

> Hi,
>
> I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file
> of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When you
> google it, it is mentioned that insuline has 2 chains named A,B. So why
> it's pdb code has 4 chains? Are they couple of each other? If yes and i
> should remove C,D chains, is there any tool to remove them standardly
> ;)(not manually)?
>
> How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
> starting simulation?
>
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Re: [gmx-users] PDB code

[Nick Johans]

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp, the
system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work with
-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
What does it mean  "protonated" ? How they add H when they have used AMBER
forcefield?
 Would you please help me?

Best regards
On Wed, 29 Aug 2018, 19:50 Nick Johans,  wrote:

> Hi,
>
> I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file
> of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When you
> google it, it is mentioned that insuline has 2 chains named A,B. So why
> it's pdb code has 4 chains? Are they couple of each other? If yes and i
> should remove C,D chains, is there any tool to remove them standardly
> ;)(not manually)?
>
> How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
> starting simulation?
>
-- 
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[gmx-users] PDB code

[Nick Johans]

Hi,

I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file
of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When you
google it, it is mentioned that insuline has 2 chains named A,B. So why
it's pdb code has 4 chains? Are they couple of each other? If yes and i
should remove C,D chains, is there any tool to remove them standardly
;)(not manually)?

How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
starting simulation?
-- 
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Re: [gmx-users] restrain ligand in free energy.

[hoangtung9597]

Tks for your reply. But this restrain -fc 1000 1000 1000 i ready know  it is 
using for nvt npt . But for md run. They don't use that restrain. Because i am 
going to calculate free energy. Dental G restrain on . 
 Tin nhắn gốc Từ: Bratin Kumar Das 
<177cy500.bra...@nitk.edu.in> Ngày: 29/08/2018  19:05  (GMT+07:00) Đến: 
gmx-us...@gromacs.org Chủ đề: Re: [gmx-users] restrain ligand in free energy. 
Hi ,
  Gromacs has genrestr programme...In protein-ligand complex tutorial
it is mentioned(how to restrain ligand)
The command is
gmx genrestr -f ligand.gro -o ligand_posre.itp -fc 1000 1000 1000
After that you need to include in the main topology

On Wed 29 Aug, 2018, 12:37 PM Tùng Hoàng,  wrote:

> Hello everyone,
> i am trying to calculate free energy for complex protein-ligand. but in
> tutorial it just have methane in water. So i find this
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> but the problem is i don know how to restrain this ligand.
> in file complex.top i see that intramolecular - interaction , bond, angle ,
> diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i can
> restrain like this . where i can find intramolecular -interaction/
> Thank you for your help.
>
> Regrads,
> Tung,
>
> --
> Hoàng Tùng / student
> hoangtung9...@gmail.com / +(84) 0928 478 789
>
> University of Medicine and Pharmacy I Ho Chi Minh City
> 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> 
>
> [image: Facebook]   [image: Skype]
> 
> --
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Re: [gmx-users] Gromacs 2018.3 install warning

[Du, Yu]

All right. Thanks for reply.

At2018-08-29 20:04:49,Paul bauerwrote:
> Hello,
> 
> we have not yet full support for gcc-8, but this is being worked on. You 
> can disregard those warnings safely for now.
> 
> /Paul
> 
> On 29/08/2018 14:01, Du, Yu wrote:
> > Dear gmx-users,
> >
> >
> >
> >
> > I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the 
> > following warning:
> >
> >
> > `make check` with regression test set 100% passed. Hope next version will 
> > fix these warnings.
> >
> >
> > ##Warnings##
> > [ 33%] Building CXX object 
> > src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:
> >  In function ‘void make_benchmark_tprs(const char*, char**, gmx_int64_t, 
> > gmx_int64_t, real, real, real, int*, t_inputinfo*, FILE*)’:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:21:
> >  warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 
> > depends on the length of the source argument [-Wstringop-overflow=]
> >   std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
> > std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
> >   
> > ^~~
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:63:
> >  note: length computed here
> >   std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
> > std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
> >  ~~~^~~~
> > [ 33%] Building CXX object 
> > src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o
> >
> >
> > [ 35%] Building CXX object 
> > src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o
> > In function ‘void calc_cumulatives(t_UmbrellaWindow*, int, 
> > t_UmbrellaOptions*, const char*, const char*)’,
> >  inlined from ‘void do_bootstrapping(const char*, const char*, const 
> > char*, const char*, char*, double*, t_UmbrellaWindow*, int, 
> > t_UmbrellaOptions*)’ at 
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1689:29:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:16:
> >  warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 
> > depends on the length of the source argument [-Wstringop-overflow=]
> >   sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
> > std::strlen(fnhist)-4));
> >   
> > ~~~^~
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
> >  In function ‘void do_bootstrapping(const char*, const char*, const char*, 
> > const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:74:
> >  note: length computed here
> >   sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
> > std::strlen(fnhist)-4));
> > 
> > ~~~^~~~
> > In function ‘void print_histograms(const char*, t_UmbrellaWindow*, int, 
> > int, t_UmbrellaOptions*, const char*)’,
> >  inlined from ‘void do_bootstrapping(const char*, const char*, const 
> > char*, const char*, char*, double*, t_UmbrellaWindow*, int, 
> > t_UmbrellaOptions*)’ at 
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1735:29:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:16:
> >  warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 
> > depends on the length of the source argument [-Wstringop-overflow=]
> >   sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
> > std::strlen(fnhist)-4), bs_index);
> >   
> > ~~~^~~
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
> >  In function ‘void do_bootstrapping(const char*, const char*, const char*, 
> > const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
> > /share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:73:
> >  note: length computed here
> >   sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
> > std::strlen(fnhist)-4), bs_index);
> >
> > ~~~^~~~
> > [ 35%] Building CXX object 
> > src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o
> > ##Warnings##
> >
> >
> >
> > --
> > Du, Yu
> > PhD 

Re: [gmx-users] restrain ligand in free energy.

[Bratin Kumar Das]

Hi ,
  Gromacs has genrestr programme...In protein-ligand complex tutorial
it is mentioned(how to restrain ligand)
The command is
gmx genrestr -f ligand.gro -o ligand_posre.itp -fc 1000 1000 1000
After that you need to include in the main topology

On Wed 29 Aug, 2018, 12:37 PM Tùng Hoàng,  wrote:

> Hello everyone,
> i am trying to calculate free energy for complex protein-ligand. but in
> tutorial it just have methane in water. So i find this
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> but the problem is i don know how to restrain this ligand.
> in file complex.top i see that intramolecular - interaction , bond, angle ,
> diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i can
> restrain like this . where i can find intramolecular -interaction/
> Thank you for your help.
>
> Regrads,
> Tung,
>
> --
> Hoàng Tùng / student
> hoangtung9...@gmail.com / +(84) 0928 478 789
>
> University of Medicine and Pharmacy I Ho Chi Minh City
> 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> 
>
> [image: Facebook]   [image: Skype]
> 
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Gromacs 2018.3 install warning

[Paul bauer]

Hello,

we have not yet full support for gcc-8, but this is being worked on. You 
can disregard those warnings safely for now.


/Paul

On 29/08/2018 14:01, Du, Yu wrote:

Dear gmx-users,




I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the following 
warning:


`make check` with regression test set 100% passed. Hope next version will fix 
these warnings.


##Warnings##
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:
 In function ‘void make_benchmark_tprs(const char*, char**, gmx_int64_t, 
gmx_int64_t, real, real, real, int*, t_inputinfo*, FILE*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:21:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
  std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
  
^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:63:
 note: length computed here
  std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
 ~~~^~~~
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o


[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o
In function ‘void calc_cumulatives(t_UmbrellaWindow*, int, t_UmbrellaOptions*, 
const char*, const char*)’,
 inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1689:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
  sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));
  
~~~^~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:74:
 note: length computed here
  sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));

~~~^~~~
In function ‘void print_histograms(const char*, t_UmbrellaWindow*, int, int, 
t_UmbrellaOptions*, const char*)’,
 inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1735:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
  sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
  
~~~^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:73:
 note: length computed here
  sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
   
~~~^~~~
[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o
##Warnings##



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275



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[gmx-users] Gromacs 2018.3 install warning

[Du, Yu]

Dear gmx-users,




I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the following 
warning:


`make check` with regression test set 100% passed. Hope next version will fix 
these warnings.


##Warnings##
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:
 In function ‘void make_benchmark_tprs(const char*, char**, gmx_int64_t, 
gmx_int64_t, real, real, real, int*, t_inputinfo*, FILE*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:21:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
 std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
 
^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:63:
 note: length computed here
 std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
~~~^~~~
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o


[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o
In function ‘void calc_cumulatives(t_UmbrellaWindow*, int, t_UmbrellaOptions*, 
const char*, const char*)’,
inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1689:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
 sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));
 
~~~^~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:74:
 note: length computed here
 sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));
   
~~~^~~~
In function ‘void print_histograms(const char*, t_UmbrellaWindow*, int, int, 
t_UmbrellaOptions*, const char*)’,
inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1735:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
 sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
 
~~~^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:73:
 note: length computed here
 sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
  
~~~^~~~
[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o
##Warnings##



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China. 
Zip: 200032, Tel: (86) 021 5492 5275
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89

[Dan Gil]

I think that may indicate that their is something wrong with your input
files, possibly the configuration.

Did you check if the configuration has any bad contacts?

On Wed, Aug 29, 2018 at 7:15 AM sagar bathla  wrote:

> hi Dan,
>
> I got the warnings at the start of the mdrun.
>
> Regards
> Sagar
>
> On Wed, Aug 29, 2018 at 3:30 PM <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
>
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users@maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> > gromacs.org_gmx-users-ow...@maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. free energy of complex system (abhisek Mondal)
> >2.  restrain ligand in free energy. (T?ng Ho?ng)
> >3. Re: rotation of atoms by more than 90 degrees & LINCS
> >   Warnings (Dan Gil)
> >4. Re: rotation of atoms by more than 90 degrees & LINCS
> >   Warnings (Dan Gil)
> >
> >
> > --
> >
> > Message: 1
> > Date: Wed, 29 Aug 2018 11:23:16 +0530
> > From: abhisek Mondal 
> > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] free energy of complex system
> > Message-ID:
> >  > f3+ulyykpn2zi3xg38dctm...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi,
> > I'm just trying to calculate free energy of a complex system using
> > following method:
> >
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
> >
> > However, I'm facing some difficulties understanding how can I achieve the
> > goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> > 0.05 spacing for data collection.
> >
> > Now, if I would like to calculate free energy of a complex (say, dimeric
> > protein) then how am I supposed to design the lambda states ?
> > I mean will it be like, one monomer will remain constant and the other
> > monomer goes from lambda=0 to 1 state ? If that be the case then please
> > suggest a way to customize the procedure.
> >
> > Please provide some suggestions.
> > I'm really willing to apply this method in my scenario.
> > Thank you.
> > --
> > Abhisek Mondal
> >
> > *Senior Research Fellow*
> > *Protein Crystallography Group*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> >
> >
> > --
> >
> > Message: 2
> > Date: Wed, 29 Aug 2018 14:06:31 +0700
> > From: T?ng Ho?ng 
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users]  restrain ligand in free energy.
> > Message-ID:
> > <
> > cafn5yuf4myt_q-xfn5qkdavn25oouj4srw-bele21grnoyk...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hello everyone,
> > i am trying to calculate free energy for complex protein-ligand. but in
> > tutorial it just have methane in water. So i find this
> >
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> > but the problem is i don know how to restrain this ligand.
> > in file complex.top i see that intramolecular - interaction , bond,
> angle ,
> > diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i
> can
> > restrain like this . where i can find intramolecular -interaction/
> > Thank you for your help.
> >
> > Regrads,
> > Tung,
> >
> > --
> > Ho?ng T?ng / student
> > hoangtung9...@gmail.com / +(84) 0928 478 789
> >
> > University of Medicine and Pharmacy I Ho Chi Minh City
> > 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> > 
> >
> > [image: Facebook]   [image: Skype]
> > 
> >
> >
> > --
> >
> > Message: 3
> > Date: Wed, 29 Aug 2018 05:56:14 -0400
> > From: Dan Gil 
> > To: gmx-us...@gromacs.org
> > Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> > LINCS   Warnings
> > Message-ID:
> >  > hog...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Hi Sagar,
> >
> > At which time step do you get LINCS warnings?
> >
> > Also, please see:
> >
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
> >
> > Dan
> >
> > On Tue, Aug 28, 2018 at 3:19 AM sagar bathla 
> > wrote:
> >
> > > Dear all,
> > >
> > > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > > 

[gmx-users] DNA simulation and choice of temperature coupling groups

[Athina Meletiou]

Hello all,

I was looking into performing some MD simulations of a DNA molecule - as a 
control to simulations of the same DNA molecule along with its binding protein. 
However I’m getting a bit confused about how to use temperature coupling 
groups. I am torn between simply using one group (“System”) or two groups 
(“DNA” and “Water_and_ions”). I’m leaning towards a single group (“System”) and 
that’s because 1) the groups I have used for the DNA and binding protein 
simulations were “Protein” and “Non-protein”, meaning that in those my DNA 
molecule was grouped together with the solvent and ions. Therefore for 
comparability I’m thinking that using “System” for the DNA simulations may be 
best. Also 2) using one group for the solute (DNA) and another for the solvent 
(Water_and_ions) can introduce artifacts into the conformational dynamics of my 
DNA molecule.

I would appreciate any insights/hints, thank you all in advance.

Kind regards,
Athina




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Re: [gmx-users] free energy of complex system

[Dallas Warren]

What Gibbs energy are you trying to calculate for the system? Of what
process or transformation?

On Wed, 29 Aug. 2018, 3:56 pm abhisek Mondal, 
wrote:

> Hi,
> I'm just trying to calculate free energy of a complex system using
> following method:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
>
> However, I'm facing some difficulties understanding how can I achieve the
> goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> 0.05 spacing for data collection.
>
> Now, if I would like to calculate free energy of a complex (say, dimeric
> protein) then how am I supposed to design the lambda states ?
> I mean will it be like, one monomer will remain constant and the other
> monomer goes from lambda=0 to 1 state ? If that be the case then please
> suggest a way to customize the procedure.
>
> Please provide some suggestions.
> I'm really willing to apply this method in my scenario.
> Thank you.
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
> *Protein Crystallography Group*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89

[sagar bathla]

hi Dan,

I got the warnings at the start of the mdrun.

Regards
Sagar

On Wed, Aug 29, 2018 at 3:30 PM <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>
> You can reach the person managing the list at
> gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. free energy of complex system (abhisek Mondal)
>2.  restrain ligand in free energy. (T?ng Ho?ng)
>3. Re: rotation of atoms by more than 90 degrees & LINCS
>   Warnings (Dan Gil)
>4. Re: rotation of atoms by more than 90 degrees & LINCS
>   Warnings (Dan Gil)
>
>
> --
>
> Message: 1
> Date: Wed, 29 Aug 2018 11:23:16 +0530
> From: abhisek Mondal 
> To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] free energy of complex system
> Message-ID:
>  f3+ulyykpn2zi3xg38dctm...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
> I'm just trying to calculate free energy of a complex system using
> following method:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
>
> However, I'm facing some difficulties understanding how can I achieve the
> goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> 0.05 spacing for data collection.
>
> Now, if I would like to calculate free energy of a complex (say, dimeric
> protein) then how am I supposed to design the lambda states ?
> I mean will it be like, one monomer will remain constant and the other
> monomer goes from lambda=0 to 1 state ? If that be the case then please
> suggest a way to customize the procedure.
>
> Please provide some suggestions.
> I'm really willing to apply this method in my scenario.
> Thank you.
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
> *Protein Crystallography Group*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
>
> --
>
> Message: 2
> Date: Wed, 29 Aug 2018 14:06:31 +0700
> From: T?ng Ho?ng 
> To: gmx-us...@gromacs.org
> Subject: [gmx-users]  restrain ligand in free energy.
> Message-ID:
> <
> cafn5yuf4myt_q-xfn5qkdavn25oouj4srw-bele21grnoyk...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello everyone,
> i am trying to calculate free energy for complex protein-ligand. but in
> tutorial it just have methane in water. So i find this
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> but the problem is i don know how to restrain this ligand.
> in file complex.top i see that intramolecular - interaction , bond, angle ,
> diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i can
> restrain like this . where i can find intramolecular -interaction/
> Thank you for your help.
>
> Regrads,
> Tung,
>
> --
> Ho?ng T?ng / student
> hoangtung9...@gmail.com / +(84) 0928 478 789
>
> University of Medicine and Pharmacy I Ho Chi Minh City
> 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> 
>
> [image: Facebook]   [image: Skype]
> 
>
>
> --
>
> Message: 3
> Date: Wed, 29 Aug 2018 05:56:14 -0400
> From: Dan Gil 
> To: gmx-us...@gromacs.org
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> LINCS   Warnings
> Message-ID:
>  hog...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Sagar,
>
> At which time step do you get LINCS warnings?
>
> Also, please see:
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
>
> Dan
>
> On Tue, Aug 28, 2018 at 3:19 AM sagar bathla 
> wrote:
>
> > Dear all,
> >
> > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > triclinic box filled with water. when i am trying to run equillibration
> > then i am getting too many lincs warnings and simulation has been getting
> > crashed everytime. i have put retraint on all atoms of graphene but still
> > this problem is occuring again.
> >
> > My .mdp file looks like this
> > title   = OPLS Graphene IN WATER NVT equilibration
> > define  = -DPOSRES -DFLEXIBLE   ; position restrain the protein
> >
> > ; Run parameters
> > integrator  = md; leap-frog 

Re: [gmx-users] rotation of atoms by more than 90 degrees & LINCS Warnings

[Dan Gil]

Hi Sagar,

At which time step do you get LINCS warnings?

Also, please see:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Dan

On Tue, Aug 28, 2018 at 3:19 AM sagar bathla  wrote:

> Dear all,
>
> My system consists of 2 orthorhombic parallel graphene sheets in a big
> triclinic box filled with water. when i am trying to run equillibration
> then i am getting too many lincs warnings and simulation has been getting
> crashed everytime. i have put retraint on all atoms of graphene but still
> this problem is occuring again.
>
> My .mdp file looks like this
> title   = OPLS Graphene IN WATER NVT equilibration
> define  = -DPOSRES -DFLEXIBLE   ; position restrain the protein
>
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 50; 2 * 50 = 1000 ps
>
> dt  = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 1000  ; save coordinates every 1.0 ps
> nstvout = 1000  ; save velocities every 1.0 ps
> nstenergy   = 1000  ; save energies every 1.0 ps
> nstlog  = 1000  ; update log file every 1.0 ps
>
> ; Bond parameters
> continuation= yes   ; first dynamics run
> constraint_algorithm= lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H
> bonds) constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> lincs-warnangle = 90
>
> ; Neighborsearching
> vdw-modifier= Force-switch
> cutoff-scheme   = Verlet
> ns_type = grid  ; search neighboring grid cells
> nstlist = 10; 20 fs, largely irrelevant with
> Verlet
> rcoulomb= 1.2   ; short-range electrostatic cutoff
> (in nm)
> rvdw= 1.2
> rlist   = 1.2   ; short-range van der Waals cutoff
> (in nm)
> rvdw-switch = 1.0
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
>
> ; Temperature coupling is on
> tcoupl  = nose-hoover   ; nose-hoover thermostat
> tc-grps = GRA SOL   ; two coupling groups - more accurate
> tau_t   = 0.1 0.1   ; time constant, in ps
> ref_t   = 300 300   ; reference temperature, one for
> each group, in K
>
> ; Pressure coupling is off
> pcoupl  = no; no pressure coupling in NVT
>
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> periodic-molecules = yes
>
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
>
> ; number of steps for center of mass motion removal =
> comm-mode= Linear
> nstcomm  = 1
> comm-grps= GRA SOL
> ; Velocity generation
> gen_vel = no; assign velocities from Maxwell
> distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
> ;non equillibrium md
> freezegrps: GRA
> freezedim: Y Y Y
>  i have tried various things but nothing is working.
> please help to solve this problem
>
> Regards
> Sagar Bathla
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] restrain ligand in free energy.

[Tùng Hoàng]

Hello everyone,
i am trying to calculate free energy for complex protein-ligand. but in
tutorial it just have methane in water. So i find this
http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
but the problem is i don know how to restrain this ligand.
in file complex.top i see that intramolecular - interaction , bond, angle ,
diheral.  and in .mdp file i see bonds_lambda increase.  I wonder how i can
restrain like this . where i can find intramolecular -interaction/
Thank you for your help.

Regrads,
Tung,

-- 
Hoàng Tùng / student
hoangtung9...@gmail.com / +(84) 0928 478 789

University of Medicine and Pharmacy I Ho Chi Minh City
197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City


[image: Facebook]   [image: Skype]

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