[gmx-users] Simulation of pure water

[G R]

Dear all,

I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
easily pdb2gmx to generate the topology file? 3) Which Forcefield is better
for this calculation?

I'v already read some tutorial, but if you have any suggestion it woulb be
appreciated.

Thank you in advance
 GR
-- 
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.

Re: [gmx-users] RMSD analysis

[RAHUL SURESH]

Dear Justin

I think I have confused so much.
Let me try to put it in simple way.

1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of
monomer(just protein) to explain stability?

2. Time step of monomer(just protein) simulation is 150ns and
protein-ligand complex is 50ns. In this case is it valid to compare the
above analyses between monomer and complex?

Dear Justin I apologise if I am not to your mark to explain in better way.




On Wed, 7 Jun 2017 at 1:19 AM, Justin Lemkul  wrote:

>
>
> On 6/6/17 1:11 PM, RAHUL SURESH wrote:
> > Dear Justin
> >
> > Thank you. I am considering  Rmsd rmsf rg as just supplementary analysis
> > for my study.  My aim to analyse  conformational change in protein. I
> would
> > like to bring a note on protein stability after ligand binding. I don't
> > know to which part of monomer I can compare the rmsd of complex with.
> > First 50ns or last .. can you please help me with this?
>
> I'm not following.  You're talking about monomers and time intervals as if
> they're interchangeable.  What's the story?  Do you have a multimer?  Are
> you
> curious about demonstrating convergence?
>
> -Justin
>
> > On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 6/6/17 2:12 AM, RAHUL SURESH wrote:
> >>> Dear Users
> >>>
> >>> *Exp procedure:*
> >>> I have simulated the protein monomer for 150ns. Using the 150ns
> >> conformer,
> >>> ligand is docked to the protein using autodock and the simulation is
> >>> carried out for 50ns.
> >>>
> >>> *Analysis:*
> >>>
> >>> Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
> >>> with that of monomer? If yes which part of the monomer trajectory
> should
> >> be
> >>> considered.?
> >>>
> >>
> >> This is up to you to determine in light of whatever your goals are in
> >> running
> >> the simulation.  What are you trying to test or determine?  Unless the
> >> protein's
> >> stability is seriously impacted by the ligand, RMSD and Rg are useless.
> >> RMSF
> >> might be useful if there are motions that are amplified or damped by
> ligand
> >> binding.  Run the analysis and see what happens on a per-residue basis.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.

Re: [gmx-users] RMSD analysis

[Justin Lemkul]

On 6/6/17 1:11 PM, RAHUL SURESH wrote:

Dear Justin

Thank you. I am considering  Rmsd rmsf rg as just supplementary analysis
for my study.  My aim to analyse  conformational change in protein. I would
like to bring a note on protein stability after ligand binding. I don't
know to which part of monomer I can compare the rmsd of complex with.
First 50ns or last .. can you please help me with this?


I'm not following.  You're talking about monomers and time intervals as if 
they're interchangeable.  What's the story?  Do you have a multimer?  Are you 
curious about demonstrating convergence?


-Justin


On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul  wrote:




On 6/6/17 2:12 AM, RAHUL SURESH wrote:

Dear Users

*Exp procedure:*
I have simulated the protein monomer for 150ns. Using the 150ns

conformer,

ligand is docked to the protein using autodock and the simulation is
carried out for 50ns.

*Analysis:*

Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
with that of monomer? If yes which part of the monomer trajectory should

be

considered.?



This is up to you to determine in light of whatever your goals are in
running
the simulation.  What are you trying to test or determine?  Unless the
protein's
stability is seriously impacted by the ligand, RMSD and Rg are useless.
RMSF
might be useful if there are motions that are amplified or damped by ligand
binding.  Run the analysis and see what happens on a per-residue basis.

-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Usage of position restraint during FEP calculation

[Justin Lemkul]

On 6/6/17 3:45 PM, Геннадий Макаров wrote:

Dear GROMACS users, I want to estimate binding free energy for small ligand 
using procedure from article doi:10.1021/jp0217839 that imlies application of 
one distance, two angle and three dihedral restraints to ligand relatively to 
receptor. These restraints are controlled by option

restraint-lambdas

in *.mdp file, which value varies from 0.0 in source, unrestrained state, to 
1.0 in target,  restrained state. But does this value affect position 
restraints? I need them to restraint part of my receptor. And, if value of 
restraint-lambdas affects position restraints, how can I exclude this affect? 
Shall I use six force constants for every position restraint statement in my 
FEP topology instead of three in usual one?




Quoting the manual for restraint-lambdas:

http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#free-energy-calculations

"Only the restraint interactions: dihedral restraints, and the pull code 
restraints are controlled with this component of the lambda vector."


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] metal ions in equilibration step

[Justin Lemkul]

On 6/6/17 8:22 AM, Mahboobeh Eslami wrote:

Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are 
two calcium ions in the protein structure. These ions play an important role. 
In the equilibration step,  should I consider protein,ligand and calcium ions 
as one single entity (for tc_grps option)? or should I consider these calcium 
as the part of ions in sol-ions group?ThanksBest



I consider structural ions to be part of the protein, not part of the bulk 
solution.

-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Usage of position restraint during FEP calculation

[Геннадий Макаров]

Dear GROMACS users, I want to estimate binding free energy for small ligand 
using procedure from article doi:10.1021/jp0217839 that imlies application of 
one distance, two angle and three dihedral restraints to ligand relatively to 
receptor. These restraints are controlled by option 

restraint-lambdas

in *.mdp file, which value varies from 0.0 in source, unrestrained state, to 
1.0 in target,  restrained state. But does this value affect position 
restraints? I need them to restraint part of my receptor. And, if value of 
restraint-lambdas affects position restraints, how can I exclude this affect? 
Shall I use six force constants for every position restraint statement in my 
FEP topology instead of three in usual one?


-- 
Геннадий Макаров
-- 
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.

[gmx-users] Energy Minimisation

[Pandya, Akash]

Hi all,

I have used the steepest descent method to minimise my system. It kept saying 
certain water molecules could not be settled but it still managed to reached 
the maximum force. Then I used the Conjugate gradient method and I get this 
error message. Can someday please tell me how I would check and ultimately get 
rid of the bad contacts.

Fatal error:
The coordinates could not be constrained. Minimizer 'cg' can not handle
constraint failures, use minimizer 'steep' before using 'cg'.



Akash






-- 
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.

[gmx-users] Fw: mdp options in GROMACS 4.5.5

[‪Mohammad Roostaie‬ ‪]

Hi João,
Thank you very much. I removed this line from the mdp file.
Regards,Mohammad

  From: João Henriques 
 To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com 
 Sent: Tuesday, 6 June 2017, 20:18:51
 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5
  
Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, 
not the integration).
/J
On Tue, Jun 6, 2017 at 5:45 PM, João Henriques  
wrote:

Hi!
I'm not sure Verlet was already implemented in GMX 4.5.5, but check the manual 
for that version (or the closest one).
Cheers,
/J
On Tue, Jun 6, 2017 at 3:27 PM,  wrote:

Hi All,
I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as 
input into grompp to generate em.tpr
integrator      = steep         ; Algorithm (steep = steepest descent 
minimization)
emtol           = 1000.0        ; Stop minimization when the maximum force < 
1000.0 kJ/mol/nm
emstep      = 0.01      ; Energy step size
nsteps          = 5         ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist             = 1             ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type             = grid              ; Method to determine neighbor list 
(simple, grid)
coulombtype         = PME               ; Treatment of long range electrostatic 
interactions
rcoulomb            = 1.0               ; Short-range electrostatic cut-off
rvdw                = 1.0               ; Short-range Van der Waals cut-off
pbc                     = xyz           ; Periodic Boundary Conditions 
(yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error 
which said that the cutoff-scheme is not recognized. what should I write 
instead of "cutoff-scheme" in this version?
Thanks,Mohammad
--
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/ma ilman/listinfo/gromacs.org_gmx -users or send a 
mail to gmx-users-requ...@gromacs.org.





   

   
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] RMSD analysis

[RAHUL SURESH]

Dear Justin

Thank you. I am considering  Rmsd rmsf rg as just supplementary analysis
for my study.  My aim to analyse  conformational change in protein. I would
like to bring a note on protein stability after ligand binding. I don't
know to which part of monomer I can compare the rmsd of complex with.
First 50ns or last .. can you please help me with this?
On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul  wrote:

>
>
> On 6/6/17 2:12 AM, RAHUL SURESH wrote:
> > Dear Users
> >
> > *Exp procedure:*
> > I have simulated the protein monomer for 150ns. Using the 150ns
> conformer,
> > ligand is docked to the protein using autodock and the simulation is
> > carried out for 50ns.
> >
> > *Analysis:*
> >
> > Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
> > with that of monomer? If yes which part of the monomer trajectory should
> be
> > considered.?
> >
>
> This is up to you to determine in light of whatever your goals are in
> running
> the simulation.  What are you trying to test or determine?  Unless the
> protein's
> stability is seriously impacted by the ligand, RMSD and Rg are useless.
> RMSF
> might be useful if there are motions that are amplified or damped by ligand
> binding.  Run the analysis and see what happens on a per-residue basis.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.

Re: [gmx-users] mdp options in GROMACS 4.5.5

[João Henriques]

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
mean, not the integration).

/J

On Tue, Jun 6, 2017 at 5:45 PM, João Henriques  wrote:

> Hi!
>
> I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> manual for that version (or the closest one).
>
> Cheers,
>
> /J
>
> On Tue, Jun 6, 2017 at 3:27 PM,  wrote:
>
>> Hi All,
>> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp -
>> used as input into grompp to generate em.tpr
>> integrator  = steep ; Algorithm (steep = steepest descent
>> minimization)
>> emtol   = 1000.0; Stop minimization when the maximum
>> force < 1000.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps  = 5 ; Maximum number of (minimization) steps
>> to perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist = 1 ; Frequency to update the neighbor
>> list and long range forces
>> cutoff-scheme   = Verlet
>> ns_type = grid  ; Method to determine neighbor
>> list (simple, grid)
>> coulombtype = PME   ; Treatment of long range
>> electrostatic interactions
>> rcoulomb= 1.0   ; Short-range electrostatic
>> cut-off
>> rvdw= 1.0   ; Short-range Van der Waals
>> cut-off
>> pbc = xyz   ; Periodic Boundary Conditions
>> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error
>> which said that the cutoff-scheme is not recognized. what should I write
>> instead of "cutoff-scheme" in this version?
>> Thanks,Mohammad
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp options in GROMACS 4.5.5

[João Henriques]

Hi!

I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
manual for that version (or the closest one).

Cheers,

/J

On Tue, Jun 6, 2017 at 3:27 PM,  wrote:

> Hi All,
> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used
> as input into grompp to generate em.tpr
> integrator  = steep ; Algorithm (steep = steepest descent
> minimization)
> emtol   = 1000.0; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps  = 5 ; Maximum number of (minimization) steps
> to perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 1 ; Frequency to update the neighbor
> list and long range forces
> cutoff-scheme   = Verlet
> ns_type = grid  ; Method to determine neighbor
> list (simple, grid)
> coulombtype = PME   ; Treatment of long range
> electrostatic interactions
> rcoulomb= 1.0   ; Short-range electrostatic cut-off
> rvdw= 1.0   ; Short-range Van der Waals cut-off
> pbc = xyz   ; Periodic Boundary Conditions
> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error
> which said that the cutoff-scheme is not recognized. what should I write
> instead of "cutoff-scheme" in this version?
> Thanks,Mohammad
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp options in GROMACS 4.5.5

[‪Mohammad Roostaie‬ ‪]

Hi All,
I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as 
input into grompp to generate em.tpr
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and 
long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions 
(yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error 
which said that the cutoff-scheme is not recognized. what should I write 
instead of "cutoff-scheme" in this version?
Thanks,Mohammad
-- 
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.

[gmx-users] metal ions in equilibration step

[Mahboobeh Eslami]

Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are 
two calcium ions in the protein structure. These ions play an important role. 
In the equilibration step,  should I consider protein,ligand and calcium ions 
as one single entity (for tc_grps option)? or should I consider these calcium 
as the part of ions in sol-ions group?ThanksBest

-- 
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.

Re: [gmx-users] RMSD analysis

[Justin Lemkul]

On 6/6/17 2:12 AM, RAHUL SURESH wrote:

Dear Users

*Exp procedure:*
I have simulated the protein monomer for 150ns. Using the 150ns conformer,
ligand is docked to the protein using autodock and the simulation is
carried out for 50ns.

*Analysis:*

Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
with that of monomer? If yes which part of the monomer trajectory should be
considered.?



This is up to you to determine in light of whatever your goals are in running 
the simulation.  What are you trying to test or determine?  Unless the protein's 
stability is seriously impacted by the ligand, RMSD and Rg are useless.  RMSF 
might be useful if there are motions that are amplified or damped by ligand 
binding.  Run the analysis and see what happens on a per-residue basis.


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Generation of density curve for biphasic system

[Justin Lemkul]

On 6/6/17 2:16 AM, Debraj Das wrote:

Dear Justin,
I am getting error with
gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat

It will not write anything in that file.


If you want help solving this, you have to tell us exactly what the error was.


I have also tried gmx density , but it is giving the overall density
profile not for the individual phase.


You can get the density of any subset of the system by providing an appropriate 
index group.  gmx density prompts you to select what you want computed, so if 
you select System you won't get what you want.  But if you select each of the 
phases separately, you will.


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

[Justin Lemkul]

On 6/6/17 2:34 AM, Apramita Chand wrote:

Dear Andre,
I added around 56 molecules of urea to 966 water. The peptide is just 6
residues and I just wanted to see its preferred conformations as well as
hydrogen bonding.
I will definitely try to extend the simulation to atleast 100ns.
For the equilibration, I found that the temperature and pressure had
converged to its desired values within 10ns. Why do we need to give longer
equilbration times?



Getting the temperature and pressure to converge is a simple matter that is 
often achieved within a few hundred ps.  It does not mean you are at equilibrium 
sampling with respect to the properties of your system.  You need to do 
convergence checks of all the relevant quantities (peptide properties, 
distribution of the co-solvents, H-bonding, etc).


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Difference in properties when method of adding urea molecules is changed in a simulation box(Andr?Farias de Moura)

[Apramita Chand]

Dear Andre,
I added around 56 molecules of urea to 966 water. The peptide is just 6
residues and I just wanted to see its preferred conformations as well as
hydrogen bonding.
I will definitely try to extend the simulation to atleast 100ns.
For the equilibration, I found that the temperature and pressure had
converged to its desired values within 10ns. Why do we need to give longer
equilbration times?

Please advise.

yours sincerely
Apramita







> Message: 4
> Date: Sun, 4 Jun 2017 13:39:18 -0300
> F
>
> Hi Apramita,
>
> you have not told us how many urea molecules you have added to you system,
> neither have you told how large your peptide of interest is, but usually
> people studying denaturation of peptides use very concentrated urea
> solutions (typically 8 M or so), which are highly viscous.
>
> If this is your case, 10 ns is certainly too short for equilibration and
20
> ns is also way too short for structural sampling, I would increase both by
> maybe 5-10 fold longer if proper relaxation and sampling are expected (how
> long is long enough can be monitored by the time evolution of the
> properties of interest - only when plateaus are obtained you can begin the
> production run)
>
> Andre
>
>
> On Sun, Jun 4, 2017 at 12:39 PM, Apramita Chand 
> wrote:
>
> > Dear All,
> >





































*> > I have tested with two ways of solvating a peptide with urea-water
mixture > > Method 1: Pre-equilibrating a urea-water box and solvating the
peptide with > > -cs option with this box > > > > Method 2: Adding urea
molecules to peptide box using -ci option and then > > solvating the
resulting box with water molecules > > > > In both the methods, same number
of urea and water molecules were added . > > 10ns equilibration followed by
20ns simulation steps were carried out. > > On analysing the properties,
average number of hydrogen bonds between > > peptide-water in method 1 was
16.221 while it changed to 14.340 in Method > > 2. Similarly, number of
H-bonds between peptide-urea changed from 5.687 to > > 4.031 on switching
from Method 1 to Method 2. > > > > On checking radial distribution
functions, interaction between > > water-peptide sites were somewhat
similar for both Methods but significant > > changes were found for
peptide-urea site-site correlations. Method-1 showed > > higher
peptide-urea interaction. > > > > What could be the reason for these
discrepancies? Are both methods correct? > > I want to go on with Method-2
for further simulations because it is > > relatively simpler but Method-1
shows higher hydrogen bonding between > > sites. > > > > Please suggest. >
> > > yours sincerely, > > Apramita > > -- > > Gromacs Users mailing list*
-- 
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.

Re: [gmx-users] RMSD Matrix Error

[Apramita Chand]

Dear Mark,
Thanks for your reply. I think you're right about the space needed for
generating RMSD Matrix. I definitely was short of 160GB !!
Further, you've talked about me using highly correlated frames and that a
suitable sub-sampling might solve the problem. How would I know which
frames to use?



Message: 2
Date: Mon, 05 Jun 2017 01:37:37 +
From: Mark Abraham 
To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] RMSD Matrix error
Message-ID:

Re: [gmx-users] Generation of density curve for biphasic system

[Debraj Das]

Dear Justin,
I am getting error with
gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat

It will not write anything in that file.
I have also tried gmx density , but it is giving the overall density
profile not for the individual phase.

With regards
Arya Das


On Mon, Jun 5, 2017 at 7:58 PM, Justin Lemkul  wrote:

>
>
> On 6/5/17 10:25 AM, Debraj Das wrote:
>
>> Dear GROMACS user,
>>
>> I am trying to get the profile of density at interface for water/dodecane
>> biphasic system.
>>
>> First I have prepared my index file with the command below
>>
>> *gmx_mpi make_ndx -f confout.gro*  and it will genetare index.ndx.
>>
>> Then I have tried the command for interface density
>>
>>
>> *gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat*
>> But it will not write density.dat file.
>>
>>
> Why not?  Do you get an error?
>
> How the density profile can be generated ? Is there any other command to
>> execute ? I need help in this regards.
>>
>>
> gmx density is probably the easier option here.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
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.

[gmx-users] RMSD analysis

[RAHUL SURESH]

Dear Users

*Exp procedure:*
I have simulated the protein monomer for 150ns. Using the 150ns conformer,
ligand is docked to the protein using autodock and the simulation is
carried out for 50ns.

*Analysis:*

Is it possible to compare my RMSD, RMSF, ROG analysis of complex system
with that of monomer? If yes which part of the monomer trajectory should be
considered.?

Thank you

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
-- 
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.