[gmx-users] Recreating newer TPRs for old Gromacs

[Jernej Zidar]

Dear all,

For the purpose of a project I am trying to recreate TPRs so I can use them
with an older version of Gromacs. The TPR files in question are:
- ion channel:
https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseA.tar.gz
- lignocellulose:
https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseB.tar.gz

The two files were prepared in Gromacs 5.1.4 but I would like to use them
with Gromacs 5.0.3. I was able to output the relevant mdp parameters
and the initial structure but I have major issues with the forcefield
parameters. Is there a way to "extract" them from the TPR files or I should
contact the original authors instead?

Thanks in advance,
Jernej Zidar
-- 
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] First beta release of GROMACS 2020

[Paul bauer]

Hi GROMACS users,

The first beta release of GROMACS 2020 is available!

We are making this available to you to get an early taste of how GROMACS
2020 will look and work, and most importantly to get feedback from you
about how well things work. While we try our hardest to keep the quality of
GROMACS as high as possible, we’re human, we overlook things while doing
other things, and we need your many pairs of eyes to help build a tool that
we can all use to do good science! We really need you to test your kinds of
simulation on your hardware, both for correctness and performance. This is
particularly important if you are using "interesting" hardware or
compilers, because we can't test all of them!

Please do not use this version for doing science you plan to publish - it
needs more testing before it’s reliable enough for that. Similarly, please
don’t use this version as a base for a project that bundles or forks
GROMACS.

What new things can you expect? (See the release notes for more details.)
* Modular simulator for running a number of default simulations.
* Improved support for gmxapi Python API, version 0.1.0
* Ability to run density guided simulations.

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2019.3
is present, (as well as some fixes targeted at 2019.4),
apart from features that have been removed.

If all goes to plan, we hope to ship the final 2020 release in time for the
New Year, but that relies on people joining in and helping us test! We hope
you will consider making that contribution, so that we can continue to
deliver high-quality free simulation software that will be useful to you on
January 1.

You can find the code, manual, release notes, installation instructions and
testsuite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020-beta1.tar.gz
Documentation: http://manual.gromacs.org/documentation/2020-beta1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2020-beta1/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2020-beta1.tar.gz

Happy testing!

--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

--
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] Ligand molecule occupancy

[Justin Lemkul]

On 9/25/19 5:46 AM, Pandya, Akash wrote:

Hi,

I have multiple ligand molecules of the same type in my system. If I wanted to 
monitor the Cartesian coordinates of each individual ligand during a 
simulation, is there a Gromacs tool to do that? or do I have write a custom 
script?


You can print coordinates over time using gmx traj.

-Justin


Some background:
My purpose is to look at binding/unbinding events for each ligand individually. 
I have calculated the minimum distance between protein residues and ligands in 
my system, but this does not give the identity of the ligand (e.g. resid or 
atom number) within a particular cut-off. I used the gmx pairdist module in 
Gromacs to calculate the minimum distance.

Any guidance will be much appreciated.

Best wishes,

Akash


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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 
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] Umbrella sampling on lipid bilayer

[Justin Lemkul]

On 9/25/19 5:50 AM, Mahsa Rezaei wrote:

Dear Dr. Warren

Thanks for your response .

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane .


Distortion of membrane protein systems (elongation or compaction along 
the z-axis) with CHARMM is a bug that was recently fixed. You can either 
patch the code with the fix found at 
https://gerrit.gromacs.org/c/gromacs/+/13297 or wait for the next 
release in any of the 2018, 2019, or 2020 branches and re-run your 
simulations.


-Justin


Thank you .

Regards

Mahsa.



Does it do that without using the pull code, i.e. just performing NPT
simulation? What is physically happening? Sounds like the bilayer is
unstable. What forcefield is this?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052dallas.warren at monash.edu

-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 24 Sep 2019 at 19:50, Mahsa Rezaei https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
wrote:


* Dear gromacs users,

*>>* I am using following pull code in md simulation
*>* for pulling a ligand across the plasma membrane model.
*>* Ligand passes through the membrane,but along simulation,
*>* the size of axis z increases.
*>* My size box is 8.52807   8.52807  14.0.
*>* And the pull distance is less than one-half the length of the box vector
*>* along.pull distance is 6 nm.
*>* After simulation my size box is 8.09025   8.09025  91.84508.
*>* What should I do?
*>>* I would be very appreciated for your such kind helps.
*>>* My mdp file  :
*>* title   = Umbrella pulling simulation
*>* ; Run parameters
*>* integrator  = md
*>* dt  = 0.002
*>* tinit   = 0
*>* nsteps  = 30 ; 600 ps
*>>* ; Output parameters
*>* nstlog  = 1000
*>* nstxout = 500   ; every 1 ps
*>* nstvout = 500
*>* nstfout = 500
*>* nstxtcout   = 500; every 1 ps
*>* nstcalcenergy   = 500
*>* nstenergy   = 500
*>* ; PME electrostatics parameters
*>* coulombtype = pme
*>* ; Single-range cutoff scheme
*>* cutoff-scheme   = Verlet
*>* nstlist = 20
*>* rlist   = 1.2
*>* rcoulomb= 1.2
*>* vdwtype = Cut-off
*>* vdw-modifier= Force-switch
*>* rvdw_switch = 1.0
*>* rvdw= 1.2
*>* ; Berendsen tempearture coupling is on in two groups
*>* tcoupl  = nose-hoover
*>* tc_grps = Protein_LIG TIP3_CLA DOPC
*>* tau_t   = 1.01.0   1.0
*>* ref_t   = 303.15 303.15 303.15
*>* ; Pressure coupling is on
*>* pcoupl  = Parrinello-Rahman
*>* pcoupltype  = semiisotropic
*>* tau_p   = 5.0
*>* compressibility = 4.5e-5  4.5e-5
*>* ref_p   = 1.0 1.0
*>* refcoord_scaling= com
*>* ; Bond parameters
*>* constraints = h-bonds
*>* constraint_algorithm= LINCS
*>* continuation= yes
*>* ;
*>* nstcomm = 100
*>* comm_mode   = linear
*>* comm_grps   = Protein_LIG TIP3_CLA DOPC
*>* ; Generate velocities is off
*>* gen_vel = no
*>* ; Periodic boundary conditions are on in all directions
*>* pbc = xyz
*>>* ; Pull code
*>* pull= yes
*>* pull_ncoords= 1 ; only one reaction coordinate
*>* pull_ngroups= 2 ; two groups defining one reaction
*>* coordinate
*>* pull_group1_name= BILAYER
*>* pull_group2_name= LIG
*>* pull_coord1_type= umbrella  ; harmonic potential
*>* pull_coord1_geometry= direction
*>* pull_coord1_dim = N N Y
*>* pull_coord1_vec = 0 0 1
*>* pull_coord1_groups  = 1 2
*>* pull_coord1_start   = yes   ; define initial COM distance > 0
*>* pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
*>* pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
*>* pull_nstxout= 500; every 1 ps
*>* pull_nstfout= 500; every 1 ps
*>>>* [image: Mailtrack]
*>* <
*>* 

Re: [gmx-users] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

Dear Dr. Warren
Unfortunately,I missed your reply!

Thanks for your response .

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane .

Thank you .

Regards

Mahsa




[image: Mailtrack]

Sender
notified by
Mailtrack

09/25/19,
03:36:23 PM

On Tue, Sep 24, 2019 at 1:20 PM Mahsa Rezaei 
wrote:

> Dear gromacs users,
>
> I am using following pull code in md simulation
> for pulling a ligand across the plasma membrane model.
> Ligand passes through the membrane,but along simulation,
> the size of axis z increases.
> My size box is 8.52807   8.52807  14.0.
> And the pull distance is less than one-half the length of the box vector
> along.pull distance is 6 nm.
> After simulation my size box is 8.09025   8.09025  91.84508.
> What should I do?
>
> I would be very appreciated for your such kind helps.
>
> My mdp file  :
> title   = Umbrella pulling simulation
> ; Run parameters
> integrator  = md
> dt  = 0.002
> tinit   = 0
> nsteps  = 30 ; 600 ps
>
> ; Output parameters
> nstlog  = 1000
> nstxout = 500   ; every 1 ps
> nstvout = 500
> nstfout = 500
> nstxtcout   = 500; every 1 ps
> nstcalcenergy   = 500
> nstenergy   = 500
> ; PME electrostatics parameters
> coulombtype = pme
> ; Single-range cutoff scheme
> cutoff-scheme   = Verlet
> nstlist = 20
> rlist   = 1.2
> rcoulomb= 1.2
> vdwtype = Cut-off
> vdw-modifier= Force-switch
> rvdw_switch = 1.0
> rvdw= 1.2
> ; Berendsen tempearture coupling is on in two groups
> tcoupl  = nose-hoover
> tc_grps = Protein_LIG TIP3_CLA DOPC
> tau_t   = 1.01.0   1.0
> ref_t   = 303.15 303.15 303.15
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman
> pcoupltype  = semiisotropic
> tau_p   = 5.0
> compressibility = 4.5e-5  4.5e-5
> ref_p   = 1.0 1.0
> refcoord_scaling= com
> ; Bond parameters
> constraints = h-bonds
> constraint_algorithm= LINCS
> continuation= yes
> ;
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = Protein_LIG TIP3_CLA DOPC
> ; Generate velocities is off
> gen_vel = no
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
>
> ; Pull code
> pull= yes
> pull_ncoords= 1 ; only one reaction coordinate
> pull_ngroups= 2 ; two groups defining one reaction
> coordinate
> pull_group1_name= BILAYER
> pull_group2_name= LIG
> pull_coord1_type= umbrella  ; harmonic potential
> pull_coord1_geometry= direction
> pull_coord1_dim = N N Y
> pull_coord1_vec = 0 0 1
> pull_coord1_groups  = 1 2
> pull_coord1_start   = yes   ; define initial COM distance > 0
> pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> pull_nstxout= 500; every 1 ps
> pull_nstfout= 500; every 1 ps
>
>
> [image: Mailtrack]
> 
>  Sender
> notified by
> Mailtrack
> 
>  09/24/19,
> 01:19:54 PM
>
-- 
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] Umbrella sampling on lipid bilayer

[Mahsa Rezaei]

Dear Dr. Warren

Thanks for your response .

I made my protein-membrane system with charmm-gui.

so my force is charmm36.

I used the equilibration input files that charmm-gui provide ,

and run 400 ns simulation for equilibration of my system .

RMSD , temperature and pressure is good , so I think my system is stable .

Every thing is good until I use following pull code in my mdp file .

The bilayer does not move and the ligand passes through the membrane

But over time , the length of the z axis increases , and

4 water molecules are also separated from the membrane .

Thank you .

Regards

Mahsa.



Does it do that without using the pull code, i.e. just performing NPT
simulation? What is physically happening? Sounds like the bilayer is
unstable. What forcefield is this?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052dallas.warren at monash.edu

-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 24 Sep 2019 at 19:50, Mahsa Rezaei https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
wrote:

>* Dear gromacs users,
*>>* I am using following pull code in md simulation
*>* for pulling a ligand across the plasma membrane model.
*>* Ligand passes through the membrane,but along simulation,
*>* the size of axis z increases.
*>* My size box is 8.52807   8.52807  14.0.
*>* And the pull distance is less than one-half the length of the box vector
*>* along.pull distance is 6 nm.
*>* After simulation my size box is 8.09025   8.09025  91.84508.
*>* What should I do?
*>>* I would be very appreciated for your such kind helps.
*>>* My mdp file  :
*>* title   = Umbrella pulling simulation
*>* ; Run parameters
*>* integrator  = md
*>* dt  = 0.002
*>* tinit   = 0
*>* nsteps  = 30 ; 600 ps
*>>* ; Output parameters
*>* nstlog  = 1000
*>* nstxout = 500   ; every 1 ps
*>* nstvout = 500
*>* nstfout = 500
*>* nstxtcout   = 500; every 1 ps
*>* nstcalcenergy   = 500
*>* nstenergy   = 500
*>* ; PME electrostatics parameters
*>* coulombtype = pme
*>* ; Single-range cutoff scheme
*>* cutoff-scheme   = Verlet
*>* nstlist = 20
*>* rlist   = 1.2
*>* rcoulomb= 1.2
*>* vdwtype = Cut-off
*>* vdw-modifier= Force-switch
*>* rvdw_switch = 1.0
*>* rvdw= 1.2
*>* ; Berendsen tempearture coupling is on in two groups
*>* tcoupl  = nose-hoover
*>* tc_grps = Protein_LIG TIP3_CLA DOPC
*>* tau_t   = 1.01.0   1.0
*>* ref_t   = 303.15 303.15 303.15
*>* ; Pressure coupling is on
*>* pcoupl  = Parrinello-Rahman
*>* pcoupltype  = semiisotropic
*>* tau_p   = 5.0
*>* compressibility = 4.5e-5  4.5e-5
*>* ref_p   = 1.0 1.0
*>* refcoord_scaling= com
*>* ; Bond parameters
*>* constraints = h-bonds
*>* constraint_algorithm= LINCS
*>* continuation= yes
*>* ;
*>* nstcomm = 100
*>* comm_mode   = linear
*>* comm_grps   = Protein_LIG TIP3_CLA DOPC
*>* ; Generate velocities is off
*>* gen_vel = no
*>* ; Periodic boundary conditions are on in all directions
*>* pbc = xyz
*>>* ; Pull code
*>* pull= yes
*>* pull_ncoords= 1 ; only one reaction coordinate
*>* pull_ngroups= 2 ; two groups defining one reaction
*>* coordinate
*>* pull_group1_name= BILAYER
*>* pull_group2_name= LIG
*>* pull_coord1_type= umbrella  ; harmonic potential
*>* pull_coord1_geometry= direction
*>* pull_coord1_dim = N N Y
*>* pull_coord1_vec = 0 0 1
*>* pull_coord1_groups  = 1 2
*>* pull_coord1_start   = yes   ; define initial COM distance > 0
*>* pull_coord1_rate= 0.01  ; 0.01 nm per ps =10nm per ns
*>* pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
*>* pull_nstxout= 500; every 1 ps
*>* pull_nstfout= 500; every 1 ps
*>>>* [image: Mailtrack]
*>* <
*>* 
https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;

*>* >
*>* Sender
*>* notified by
*>* Mailtrack
*>* <
*>* 
https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;

*>* >
*>* 09/24/19,
*>* 01:19:54 PM
*>* --
*>* Gromacs 

[gmx-users] Ligand molecule occupancy

[Pandya, Akash]

Hi,

I have multiple ligand molecules of the same type in my system. If I wanted to 
monitor the Cartesian coordinates of each individual ligand during a 
simulation, is there a Gromacs tool to do that? or do I have write a custom 
script?

Some background:
My purpose is to look at binding/unbinding events for each ligand individually. 
I have calculated the minimum distance between protein residues and ligands in 
my system, but this does not give the identity of the ligand (e.g. resid or 
atom number) within a particular cut-off. I used the gmx pairdist module in 
Gromacs to calculate the minimum distance.

Any guidance will be much appreciated.

Best wishes,

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.

Re: [gmx-users] issues running virus capsid simulation

[David van der Spoel]

Den 2019-09-25 kl. 02:37, skrev Justin Lemkul:



On 9/24/19 5:09 PM, Asis Jana wrote:

Hi,

I am doing viral capsid simulation using GROMACS 2018. The capsid was 
first
energy minimized using the steepest-descent algorithm followed by 40 
ns of

NVT (300 K) followed by 10 ns of NPT (300 K, 1 atm) equilibration. In the
NVT and NPT equilibration, the heavy atoms of the protein were restrained
with a force constant of 1000 kJ/mol/nm. Production MD simulations were
performed for 400 ns at a temperature of 300 K and a pressure of 1 atm.
Please see the production mdp file below.

title   = MD simulation
; Run parameters
integrator  = md
nsteps  = 20
dt  = 0.002
; Output control
nstxout = 5
nstvout = 5
nstenergy   = 5
nstlog  = 5
nstxout-compressed  = 5

compressed-x-grps   = System

continuation    = yes
constraint_algorithm    = lincs
constraints = h-bonds
lincs_iter  = 1
lincs_order = 4
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid
nstlist = 20
rlist   = 1.2
coulombtype = pme
rcoulomb    = 1.2
vdwtype = Cut-off
vdw-modifier    = Force-switch
rvdw_switch = 1.0
rvdw    = 1.2
pme_order   = 4
fourierspacing  = 0.16
; Temperature coupling is on
tcoupl  = Nose-Hoover
tc-grps = Protein Non-Protein
tau_t   = 1.0 1.0
ref_t   = 300 300
; Pressure coupling is on
pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 5.0
ref_p   = 1.0
compressibility = 4.5e-5
refcoord_scaling    = com
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no    ; Velocity generation is off
nstcomm = 100
comm_mode   = linear
comm_grps   = Protein Non-Protein

I have attached RMSD and Rg plots with this mail. It looks like that 
capsid

is stiil not equilibrated. Rg is increasing rapidly, whereas RMSD of the
capsid is increasing slowly. Please see the attached plots.  Any kind of
advice or suggestions are deeply appreciated.


The mailing list does not accept attachments. To share images, upload 
them to a file-sharing service and provide a URL.


What do your eyes tell you when you visualize the trajectory? Do the 
data make sense? Have you accounted for periodicity effects? Are there 
simply structural changes happening? Nothing says any structural metric 
has to level off in some convenient amount of time.




Indeed, big things take long time to equilibrate. For a virus it may 
depend on whether a genome is present, ions etc. We did this stuff8 
years ago and it take many microseconds:


https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002502

https://pubs.acs.org/doi/abs/10.1021/ct3002128


-Justin




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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.