Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Justin Lemkul]

Please don't reply to entire digests.

On 5/15/16 4:48 AM, Antara mazumdar wrote:

Dear Justin,

I am using the velocities from the NPT run. Could you please explain on the
.cpt file you mentioned?



This command:

gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
MD.mdp -o MD.tpr

might preserve the low-precision velocities written to the .gro file, but it 
preserves nothing about the ensemble at the end of the equilibration run. 
Consult any basic tutorial for proper usage of grompp and continuing runs.  If 
you don't carefully continue your simulations, you're going to find all sorts of 
bizarre behavior.


-Justin


Kind Regards,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--



On Sun, May 15, 2016 at 10:51 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:


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Today's Topics:

   1. COM-Pull along a direction (Pengzhi Zhang)
   2. Re: error in running mdrun of membrane protein in a mixed
  bilayer with MARTINI MODEL (Justin Lemkul)
   3. Umbrella Sampling - choice of pull-coord?-dim (Lukas Zimmermann)
   4. PCA and FEL (sun)
   5. Re: PCA and FEL (Tsjerk Wassenaar)


--

Message: 1
Date: Sat, 14 May 2016 14:58:37 -0500
From: Pengzhi Zhang 
To: 
Subject: [gmx-users] COM-Pull along a direction
Message-ID: <5737836d.8010...@central.uh.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed

Dear Gromacs users,

I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull
the ion along specific pre-determined paths.

 From my understanding, pulling along a direction _V guarantees that the
dumb bead would move only at direction _V. The position of the dumb bead
is simply: _r(t) = _r(0) + _V*speed*time (_ means vector). And if the
spring constant is sufficiently large, the pulled atom (a single ion)
would also follow the dumb bead (with fluctuations). However, I found
that no matter how large the spring constant is (I vary it from 100 to
1,000,000 kJ/mol/nm**2), the pulled atom deviates from the direction _V
in a certain amount of time (usually after the pulled bead unbinds),
sometimes it even goes perpendicular to _V and moves out of the box,
terminating the simulation.

Does the direction _V (pull-coord1-vec) mean the direction of
instantaneous pull force or the direction of the path that the dumb bead
follows?

Thank you very much in advance!


Here is the pull part of my mdp file.
; COM PULLING
; Pull type: no, umbrella, constraint or constant-force
pull= umbrella
pull-geometry= direction
pull-ngroups  = 2
pull-ncoords  = 1
pull-group1-name  = binding_site_atoms
pull-group2-name  = pull_ion   ; pull group
pull-start= yes
pull-coord1-vec  = -0.07 -0.04 0.99
pull-coord1-groups= 1 2
pull_coord1_rate= 0.001; nm/ps
pull-coord1-k = 1   ; kJ/mol/nm^2
pull-nstxout   = 10 ; 0.02 ps
pull-nstfout= 10
pull-print-reference= yes


Sincerely,
Pengzhi


--

Message: 2
Date: Sat, 14 May 2016 18:33:08 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] error in running mdrun of membrane protein in
a mixed bilayer with MARTINI MODEL
Message-ID: <5b732333-0517-e66f-2e4b-7a9cf337e...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 5/14/16 2:34 PM, Mark Abraham wrote:

Hi,

Please keep the discussion on the mailing list, so others can help and
learn.


Antara said:
I have pasted the mdrun command i used to run it in parallel with the

number of processors i used which was 16. The command is :



/app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8


That still isn't a command you've copied and pasted from a terminal or a
script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
etc.


In the pbs script, i used 16 in the number of processors option.


What happens when you run on one rank?


For the production tpr, i used the gro file from the last equilibration

step(step6.6) The command used was :


gmx grompp -c 

Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Justin Lemkul]

On 5/14/16 2:34 PM, Mark Abraham wrote:

Hi,

Please keep the discussion on the mailing list, so others can help and
learn.


Antara said:
I have pasted the mdrun command i used to run it in parallel with the

number of processors i used which was 16. The command is :



/app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8


That still isn't a command you've copied and pasted from a terminal or a
script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
etc.


In the pbs script, i used 16 in the number of processors option.


What happens when you run on one rank?


For the production tpr, i used the gro file from the last equilibration

step(step6.6) The command used was :


gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f

MD.mdp -o MD.tpr

That looks like it could be reasonable, but as with any equilibration you
need to look at observables to judge that it's equilibrated. Their builder
should provide reasonable defaults, but you can't assume they're perfect,
either. In particular, if the last equilibration ensemble doesn't match the
production ensemble, that could be the problem.



Failing to pass the .cpt file to grompp -t after equilibration is a great way to 
do that.  The production simulation is starting from some unpredictable 
ensemble, without velocities, etc..


-Justin


Mark

On Sat, May 14, 2016 at 5:10 PM Mark Abraham 
wrote:


Hi,

On Sat, May 14, 2016 at 4:34 PM Antara mazumdar 
wrote:


Dear users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model 2.2. I have already performed all
the equilibration steps successfully on my desktop with GROMACS 5.1.0.
However, when i try to execute its production run in parallel(having
gromacs 5.1 version installed)  it complains of LINCS warning and
terminates at step 0. The lincs warning error is coming from BB and SC1
atoms of one of the protein residues.



There are lots of possible places to go wrong, including not making your
production .tpr based on the outputs of your equilibration. This seems
quite a likely possibility.

You should also consider further equilibration - whether using Martini or
not, it is sometimes necessary to use a small time step when relaxing
problem configurations.



 But on the contrary, it runs on the desktop successfully. *My production
run mdp file details are below :*


.

This is the MD.mdp file :ntegrator   = md
tinit= 0.0
dt   = 0.020
nsteps   = 25

nstxout  = 2000
nstvout  = 2000
nstfout  = 2000
nstlog   = 2000
nstenergy= 2000
nstxtcout= 2000
xtc_precision= 100

ns_type  = grid
pbc  = xyz
nstlist = 10
cutoff-scheme   = Verlet
rlist   = 1.2
vdwtype = Cut-off
vdw-modifier= none
rvdw_switch = 1.0
rvdw= 1.2
coulombtype = pme
rcoulomb= 1.2

tcoupl   = v-rescale
tc-grps  = protein CHOL_POPC_DPSM_DPCE W_ION

tau_t= 1.0 1.0  1.0
ref_t= 303.15 303.15 303.15

; Pressure coupling:
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 5.0  5.0
compressibility  = 3e-4 3e-4
ref_p= 1.0  1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel  = no
refcoord_scaling = all

*the command used for mdrun :*

-deffnm MD -pin on -rdd 1.8 -np 16



mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
Please don't edit and filture things, copy and paste whole actual things.
:-)

Mark

I would also like to mention that i generated the initial structure of the

system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
have followed the exact builder protocol for the equilibration and
minimisation.

Kindly suggest something!

Thanks,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
--
Gromacs Users mailing list

* Please search the archive at
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posting!

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

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--
==

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

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

Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Mark Abraham]

Hi,

Please keep the discussion on the mailing list, so others can help and
learn.

> Antara said:
> I have pasted the mdrun command i used to run it in parallel with the
number of processors i used which was 16. The command is :
>
>
>/app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8

That still isn't a command you've copied and pasted from a terminal or a
script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun,
etc.

> In the pbs script, i used 16 in the number of processors option.

What happens when you run on one rank?

> For the production tpr, i used the gro file from the last equilibration
step(step6.6) The command used was :
>
> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f
MD.mdp -o MD.tpr

That looks like it could be reasonable, but as with any equilibration you
need to look at observables to judge that it's equilibrated. Their builder
should provide reasonable defaults, but you can't assume they're perfect,
either. In particular, if the last equilibration ensemble doesn't match the
production ensemble, that could be the problem.

Mark

On Sat, May 14, 2016 at 5:10 PM Mark Abraham 
wrote:

> Hi,
>
> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar 
> wrote:
>
>> Dear users,
>>
>> I am trying to run a coarse grained simulation of a membrane protein in a
>> mixed lipid billayer using martini model 2.2. I have already performed all
>> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
>> However, when i try to execute its production run in parallel(having
>> gromacs 5.1 version installed)  it complains of LINCS warning and
>> terminates at step 0. The lincs warning error is coming from BB and SC1
>> atoms of one of the protein residues.
>>
>
> There are lots of possible places to go wrong, including not making your
> production .tpr based on the outputs of your equilibration. This seems
> quite a likely possibility.
>
> You should also consider further equilibration - whether using Martini or
> not, it is sometimes necessary to use a small time step when relaxing
> problem configurations.
>
>
>>  But on the contrary, it runs on the desktop successfully. *My production
>> run mdp file details are below :*
>>
>>
>> .
>>
>> This is the MD.mdp file :ntegrator   = md
>> tinit= 0.0
>> dt   = 0.020
>> nsteps   = 25
>>
>> nstxout  = 2000
>> nstvout  = 2000
>> nstfout  = 2000
>> nstlog   = 2000
>> nstenergy= 2000
>> nstxtcout= 2000
>> xtc_precision= 100
>>
>> ns_type  = grid
>> pbc  = xyz
>> nstlist = 10
>> cutoff-scheme   = Verlet
>> rlist   = 1.2
>> vdwtype = Cut-off
>> vdw-modifier= none
>> rvdw_switch = 1.0
>> rvdw= 1.2
>> coulombtype = pme
>> rcoulomb= 1.2
>>
>> tcoupl   = v-rescale
>> tc-grps  = protein CHOL_POPC_DPSM_DPCE W_ION
>>
>> tau_t= 1.0 1.0  1.0
>> ref_t= 303.15 303.15 303.15
>>
>> ; Pressure coupling:
>> Pcoupl   = berendsen
>> Pcoupltype   = semiisotropic
>> tau_p= 5.0  5.0
>> compressibility  = 3e-4 3e-4
>> ref_p= 1.0  1.0
>> ; GENERATE VELOCITIES FOR STARTUP RUN:
>> gen_vel  = no
>> refcoord_scaling = all
>>
>> *the command used for mdrun :*
>>
>> -deffnm MD -pin on -rdd 1.8 -np 16
>>
>
> mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
> Please don't edit and filture things, copy and paste whole actual things.
> :-)
>
> Mark
>
> I would also like to mention that i generated the initial structure of the
>> system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
>> have followed the exact builder protocol for the equilibration and
>> minimisation.
>>
>> Kindly suggest something!
>>
>> Thanks,
>> Antara
>>
>> --
>> Junior research fellow(project)
>> Systems biology group
>> CSIR-Institute of Genomics & Integrative Biology
>> South Campus
>> New Delhi -  110020
>> M : +91-9717970040
>> --
>> --
>> 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] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Mark Abraham]

Hi,

On Sat, May 14, 2016 at 4:34 PM Antara mazumdar 
wrote:

> Dear users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model 2.2. I have already performed all
> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> However, when i try to execute its production run in parallel(having
> gromacs 5.1 version installed)  it complains of LINCS warning and
> terminates at step 0. The lincs warning error is coming from BB and SC1
> atoms of one of the protein residues.
>

There are lots of possible places to go wrong, including not making your
production .tpr based on the outputs of your equilibration. This seems
quite a likely possibility.

You should also consider further equilibration - whether using Martini or
not, it is sometimes necessary to use a small time step when relaxing
problem configurations.


>  But on the contrary, it runs on the desktop successfully. *My production
> run mdp file details are below :*
>
>
> .
>
> This is the MD.mdp file :ntegrator   = md
> tinit= 0.0
> dt   = 0.020
> nsteps   = 25
>
> nstxout  = 2000
> nstvout  = 2000
> nstfout  = 2000
> nstlog   = 2000
> nstenergy= 2000
> nstxtcout= 2000
> xtc_precision= 100
>
> ns_type  = grid
> pbc  = xyz
> nstlist = 10
> cutoff-scheme   = Verlet
> rlist   = 1.2
> vdwtype = Cut-off
> vdw-modifier= none
> rvdw_switch = 1.0
> rvdw= 1.2
> coulombtype = pme
> rcoulomb= 1.2
>
> tcoupl   = v-rescale
> tc-grps  = protein CHOL_POPC_DPSM_DPCE W_ION
>
> tau_t= 1.0 1.0  1.0
> ref_t= 303.15 303.15 303.15
>
> ; Pressure coupling:
> Pcoupl   = berendsen
> Pcoupltype   = semiisotropic
> tau_p= 5.0  5.0
> compressibility  = 3e-4 3e-4
> ref_p= 1.0  1.0
> ; GENERATE VELOCITIES FOR STARTUP RUN:
> gen_vel  = no
> refcoord_scaling = all
>
> *the command used for mdrun :*
>
> -deffnm MD -pin on -rdd 1.8 -np 16
>

mdrun 5.1 won't accept -np, so I don't know what you are actually doing.
Please don't edit and filture things, copy and paste whole actual things.
:-)

Mark

I would also like to mention that i generated the initial structure of the
> system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
> have followed the exact builder protocol for the equilibration and
> minimisation.
>
> Kindly suggest something!
>
> Thanks,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
> --
> 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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mail to gmx-users-requ...@gromacs.org.

[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

[Antara mazumdar]

Dear users,

I am trying to run a coarse grained simulation of a membrane protein in a
mixed lipid billayer using martini model 2.2. I have already performed all
the equilibration steps successfully on my desktop with GROMACS 5.1.0.
However, when i try to execute its production run in parallel(having
gromacs 5.1 version installed)  it complains of LINCS warning and
terminates at step 0. The lincs warning error is coming from BB and SC1
atoms of one of the protein residues.

 But on the contrary, it runs on the desktop successfully. *My production
run mdp file details are below :*


.

This is the MD.mdp file :ntegrator   = md
tinit= 0.0
dt   = 0.020
nsteps   = 25

nstxout  = 2000
nstvout  = 2000
nstfout  = 2000
nstlog   = 2000
nstenergy= 2000
nstxtcout= 2000
xtc_precision= 100

ns_type  = grid
pbc  = xyz
nstlist = 10
cutoff-scheme   = Verlet
rlist   = 1.2
vdwtype = Cut-off
vdw-modifier= none
rvdw_switch = 1.0
rvdw= 1.2
coulombtype = pme
rcoulomb= 1.2

tcoupl   = v-rescale
tc-grps  = protein CHOL_POPC_DPSM_DPCE W_ION

tau_t= 1.0 1.0  1.0
ref_t= 303.15 303.15 303.15

; Pressure coupling:
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
tau_p= 5.0  5.0
compressibility  = 3e-4 3e-4
ref_p= 1.0  1.0
; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel  = no
refcoord_scaling = all

*the command used for mdrun :*

-deffnm MD -pin on -rdd 1.8 -np 16

I would also like to mention that i generated the initial structure of the
system using CHARMM GUI MARTINI MAKER protein-membrane system option. I
have followed the exact builder protocol for the equilibration and
minimisation.

Kindly suggest something!

Thanks,
Antara

--
Junior research fellow(project)
Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
--
-- 
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.