Re: [gmx-users] PCA and FEL

[Tsjerk Wassenaar]

Hi Suniba,

No, with gmx anaeig you can select -2d, which does a 2D projection onto the
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
to do that is something like:

paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
combined.xvg

You will loose the labels, but that should be fine.

You can combine other variables in a similar manner.

Hope it helps,

Tsjerk

On Sun, May 15, 2016 at 5:33 AM, sun  wrote:

> Hello everyone
> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
> for the stability of my pro-lig complex.   In a 2015 paper, The group
> calculated two principal component, PC1 and PC2 and then prepared an.xvg
> file to be used as input for g_sham. My question is, when we use g_anaeig;
> we get eigenvec.xvg. from -comp flag. Now how shall one select two
> principal components from that data? I am sorry if my question is wrong but
> please help me.
>
> My second question is, can we use any two parameters like rmsd and Rg for
> input in g_sham to probe the stability of complex? Is that valid?
>
> With Regards
> Suniba
>
> Sent from my iPhone
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[gmx-users] PCA and FEL

[sun]

Hello everyone
I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis for the 
stability of my pro-lig complex.   In a 2015 paper, The group calculated two 
principal component, PC1 and PC2 and then prepared an.xvg file to be used as 
input for g_sham. My question is, when we use g_anaeig; we get eigenvec.xvg. 
from -comp flag. Now how shall one select two principal components from that 
data? I am sorry if my question is wrong but please help me. 

My second question is, can we use any two parameters like rmsd and Rg for input 
in g_sham to probe the stability of complex? Is that valid? 

With Regards
Suniba

Sent from my iPhone
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[gmx-users] Umbrella Sampling - choice of pull-coord?-dim

[Lukas Zimmermann]

Dear GROMACS users,

I am interested in the role of the mdp parameter pull-coord?-dim when
sampling
a particular umbrella window after having generated initial configurations
for, say, the
COM distance between two groups being the reaction coordinate.

I know that these options can be controlled to restrict the actual pulling,
say with geometry distance,  to a subset of the pull vector components, for
instance to enable
aligment of the pull vector with the box dimensions.

However, I do not understand its role when performing umbrella sampling
along the reaction coordinate.
I know that the pull-code then controls the COM distance between the pull
groups with a (usually) harmonic potential, but what effect will
pull-coord?-dim have?

I observe different behavior for my toy system consisting of two methanol
molecules in vacuum.
With all components enables, I need to correct the PMF for entropic
decrease in the PMF,
since the methanol is sampled on a sphere with increasing radius.
If only allowing one component, the PMF will be flat, but different values
for delta G
result.

Also, in the US Tutorial by Justin, the US code uses:

pull_coord1_dim = N N Y

Is there any particular reason, not to set

pull_coord1_dim = Y Y Y

here? Would this setting also be justified? Since, as far as I understood
the procedure,  pulling

is just there for generating the initial configurations and US is more or
less independent of this.



Many thanks in advance!

Lukas
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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

--
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Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi -  110020
M : +91-9717970040
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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

[gmx-users] COM-Pull along a direction

[Pengzhi Zhang]

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
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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
>>
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>> 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] (no subject)

[Francesco Carbone]

I would use -dump to extract only the last frame,
I believe that what your are doing is saving your trajectory in a pdb file.



On 14 May 2016 at 16:21, Mark Abraham  wrote:

> Hi,
>
> Sure, but if you have a million frames, then you are probably doing
> something other than what you want or should do. See
>
> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
>
> Mark
>
> On Sat, May 14, 2016 at 5:15 PM Upasana Ray 
> wrote:
>
> > I have modelled my protein using homology modeling software & then have
> > used gromacs for energy minimization.
> >
> > gmx trjconv -f md22.xtc -s md22.tpr -o md22.pdb
> > then I have choosen only protein from the options
> >
> > On Sat, May 14, 2016 at 3:55 PM, Pratiti Bhadra <
> pratiti.bha...@gmail.com>
> > wrote:
> >
> > > How many frames do u save using trjconv?. Can you please post your full
> > > trjconv command here.
> > > On 14 May 2016 18:21, "Chalaoux, Francois-Regis" <
> > > francois-regis.chala...@evotec.com> wrote:
> > >
> > > > What is your protein, PDB Id ?
> > > >
> > > > FR.
> > > >
> > > > > Le 14 mai 2016 à 12:04:09, Upasana Ray  a
> > > > écrit :
> > > > >
> > > > > yes I have removed water & the pdb file only contains  protein
> > > > >
> > > > > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
> > > > > francois-regis.chala...@evotec.com> wrote:
> > > > >
> > > > >> Hi,
> > > > >>
> > > > >> Did you removed Water ?
> > > > >> Check also there is no other protein in the same file.
> > > > >>
> > > > >> FR.
> > > > >>
> > > > >>> Le 14 mai 2016 à 07:04:15, Upasana Ray 
> a
> > > > >> écrit :
> > > > >>>
> > > > >>> Dear  user,
> > > > >>>
> > > > >>> I have generated my final protein.pdb file by using trjconv
> command
> > > > from
> > > > >>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am
> > > opening
> > > > >> it
> > > > >>> for docking purpose my computer is freezing. Now how can I reduce
> > my
> > > > pdb
> > > > >>> file size  from GB to MB for using it properly. please help me to
> > > deal
> > > > >>> with this problem.
> > > > >>> --
> > > > >>> 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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> > > > >> posting!
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> > or
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> > > > >>
> > > > > --
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> > > >
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> * Please 

Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

Sure, but if you have a million frames, then you are probably doing
something other than what you want or should do. See
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Mark

On Sat, May 14, 2016 at 5:15 PM Upasana Ray  wrote:

> I have modelled my protein using homology modeling software & then have
> used gromacs for energy minimization.
>
> gmx trjconv -f md22.xtc -s md22.tpr -o md22.pdb
> then I have choosen only protein from the options
>
> On Sat, May 14, 2016 at 3:55 PM, Pratiti Bhadra 
> wrote:
>
> > How many frames do u save using trjconv?. Can you please post your full
> > trjconv command here.
> > On 14 May 2016 18:21, "Chalaoux, Francois-Regis" <
> > francois-regis.chala...@evotec.com> wrote:
> >
> > > What is your protein, PDB Id ?
> > >
> > > FR.
> > >
> > > > Le 14 mai 2016 à 12:04:09, Upasana Ray  a
> > > écrit :
> > > >
> > > > yes I have removed water & the pdb file only contains  protein
> > > >
> > > > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
> > > > francois-regis.chala...@evotec.com> wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> Did you removed Water ?
> > > >> Check also there is no other protein in the same file.
> > > >>
> > > >> FR.
> > > >>
> > > >>> Le 14 mai 2016 à 07:04:15, Upasana Ray  a
> > > >> écrit :
> > > >>>
> > > >>> Dear  user,
> > > >>>
> > > >>> I have generated my final protein.pdb file by using trjconv command
> > > from
> > > >>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am
> > opening
> > > >> it
> > > >>> for docking purpose my computer is freezing. Now how can I reduce
> my
> > > pdb
> > > >>> file size  from GB to MB for using it properly. please help me to
> > deal
> > > >>> with this problem.
> > > >>> --
> > > >>> Gromacs Users mailing list
> > > >>>
> > > >>> * Please search the archive at
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Re: [gmx-users] (no subject)

[Upasana Ray]

I have modelled my protein using homology modeling software & then have
used gromacs for energy minimization.

gmx trjconv -f md22.xtc -s md22.tpr -o md22.pdb
then I have choosen only protein from the options

On Sat, May 14, 2016 at 3:55 PM, Pratiti Bhadra 
wrote:

> How many frames do u save using trjconv?. Can you please post your full
> trjconv command here.
> On 14 May 2016 18:21, "Chalaoux, Francois-Regis" <
> francois-regis.chala...@evotec.com> wrote:
>
> > What is your protein, PDB Id ?
> >
> > FR.
> >
> > > Le 14 mai 2016 à 12:04:09, Upasana Ray  a
> > écrit :
> > >
> > > yes I have removed water & the pdb file only contains  protein
> > >
> > > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
> > > francois-regis.chala...@evotec.com> wrote:
> > >
> > >> Hi,
> > >>
> > >> Did you removed Water ?
> > >> Check also there is no other protein in the same file.
> > >>
> > >> FR.
> > >>
> > >>> Le 14 mai 2016 à 07:04:15, Upasana Ray  a
> > >> écrit :
> > >>>
> > >>> Dear  user,
> > >>>
> > >>> I have generated my final protein.pdb file by using trjconv command
> > from
> > >>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am
> opening
> > >> it
> > >>> for docking purpose my computer is freezing. Now how can I reduce my
> > pdb
> > >>> file size  from GB to MB for using it properly. please help me to
> deal
> > >>> with this problem.
> > >>> --
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Mark Abraham]

Hi,

On Sat, May 14, 2016 at 1:09 PM  wrote:

> In case it's relevant/interesting to anyone, here are the details on our
> cluster nodes:
>
> nodes   #   model   # cores cpu model
>   RAM   node_type
> fmb01 - fmb33   33  IBM HS21XM  8   3 GHz Xeon
> E5450
>  16GB   hs21
> fmb34 - fmb42   9   IBM HS228   2.4 GHz
> Xeon E5530
> 16GBhs22
> fmb43 - fmb88   45  Dell PE M6108   2.4 GHz
> Xeon E5530
>  16GB   m610
> fmb88 - fmb90   3   Dell PE M610+   12  3.4 GHz
> Xeon X5690
>   48GB  m610+
> fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9 GHz
> Xeon E5-2667
>64GB m620
> fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5 GHz
> Xeon E5-2643 v2 64GB
> m620+
> fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4 GHz
> Xeon E5-2643 v3 64GB
> m630
>
> I could only run GROMACS 4.6.2 on the last three node types and I believe
> the same is true for 5.0.4
>

Sure. GROMACS is designed to target whichever hardware was selected at
configure time, which your sysadmins for such a heterogeneous cluster
should have documented somewhere. They should also be making available to
you a mechanism to target your jobs to nodes where they can run programs
that use the hardware efficiently, or providing GROMACS installations that
work regardless of which node you are actually on. You might like to
respectfully remind them of the things we say at
http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#portability-aspects
(These thoughts are common to earlier versions also.)

Mark


Best wishes
> James
>
> > I have found that only some kinds of nodes on our cluster work for
> gromacs
> > 4.6 (the ones we call m620, m620+ and m630 but not others - I can check
> > the details tomorrow). I haven't tested it again now I'm using 5.0 so
> > don't know if that's still an issue but if it is it could explain why
> your
> > restart failed even and the initial run didn't.
> >
> >> thanks a lot for your fast response.
> >>
> >> I have tried it, and it failed. I ask in this forum just to make sure.
> >> However, there was something in my cluster that probably make it failed.
> >> I'll handle it first and then retry to restart again.
> >>
> >> Regards,
> >>
> >> Husen
> >>
> >> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul  wrote:
> >>
> >>>
> >>>
> >>> On 5/13/16 8:53 PM, Husen R wrote:
> >>>
>  Dear all
> 
>  Does simulation able to be restarted from checkpoint file with fewer
>  nodes ?
>  let's say, at the first time, I run simulation with 3 nodes. At
>  running
>  time, one of those nodes is crashed and the simulation is terminated.
> 
>  I want to restart that simulation immadiately based on checkpoint file
>  with
>  the remaining 2 nodes. does gromacs support such case ?
>  I need help.
> 
> >>>
> >>> Have you tried it?  It should work.  You will probably get a note about
> >>> the continuation not being exact due to a change in the number of
> >>> cores,
> >>> but the run should proceed fine.
> >>>
> >>> -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!
> >>>
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> >>>
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> >>> 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
> --
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[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
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[jkrieger]

In case it's relevant/interesting to anyone, here are the details on our
cluster nodes:

nodes   #   model   # cores cpu model   
 
  RAM   node_type
fmb01 - fmb33   33  IBM HS21XM  8   3 GHz Xeon 
E5450  
 16GB   hs21
fmb34 - fmb42   9   IBM HS228   2.4 GHz Xeon 
E5530 
16GBhs22
fmb43 - fmb88   45  Dell PE M6108   2.4 GHz Xeon 
E5530
 16GB   m610
fmb88 - fmb90   3   Dell PE M610+   12  3.4 GHz Xeon 
X5690   
  48GB  m610+
fmb91 - fmb202  112 Dell PE M62024 (HT) 2.9 GHz Xeon 
E5-2667
   64GB m620
fmb203 - fmb279 77  Dell PE M62024 (HT) 3.5 GHz Xeon 
E5-2643 v2 64GB
m620+
fmb280 - fmb359 80  Dell PE M63024 (HT) 3.4 GHz Xeon 
E5-2643 v3 64GB
m630

I could only run GROMACS 4.6.2 on the last three node types and I believe
the same is true for 5.0.4

Best wishes
James

> I have found that only some kinds of nodes on our cluster work for gromacs
> 4.6 (the ones we call m620, m620+ and m630 but not others - I can check
> the details tomorrow). I haven't tested it again now I'm using 5.0 so
> don't know if that's still an issue but if it is it could explain why your
> restart failed even and the initial run didn't.
>
>> thanks a lot for your fast response.
>>
>> I have tried it, and it failed. I ask in this forum just to make sure.
>> However, there was something in my cluster that probably make it failed.
>> I'll handle it first and then retry to restart again.
>>
>> Regards,
>>
>> Husen
>>
>> On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul  wrote:
>>
>>>
>>>
>>> On 5/13/16 8:53 PM, Husen R wrote:
>>>
 Dear all

 Does simulation able to be restarted from checkpoint file with fewer
 nodes ?
 let's say, at the first time, I run simulation with 3 nodes. At
 running
 time, one of those nodes is crashed and the simulation is terminated.

 I want to restart that simulation immadiately based on checkpoint file
 with
 the remaining 2 nodes. does gromacs support such case ?
 I need help.

>>>
>>> Have you tried it?  It should work.  You will probably get a note about
>>> the continuation not being exact due to a change in the number of
>>> cores,
>>> but the run should proceed fine.
>>>
>>> -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.
>>>
>> --
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>>
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>>
>
>
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Re: [gmx-users] (no subject)

[Pratiti Bhadra]

How many frames do u save using trjconv?. Can you please post your full
trjconv command here.
On 14 May 2016 18:21, "Chalaoux, Francois-Regis" <
francois-regis.chala...@evotec.com> wrote:

> What is your protein, PDB Id ?
>
> FR.
>
> > Le 14 mai 2016 à 12:04:09, Upasana Ray  a
> écrit :
> >
> > yes I have removed water & the pdb file only contains  protein
> >
> > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
> > francois-regis.chala...@evotec.com> wrote:
> >
> >> Hi,
> >>
> >> Did you removed Water ?
> >> Check also there is no other protein in the same file.
> >>
> >> FR.
> >>
> >>> Le 14 mai 2016 à 07:04:15, Upasana Ray  a
> >> écrit :
> >>>
> >>> Dear  user,
> >>>
> >>> I have generated my final protein.pdb file by using trjconv command
> from
> >>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening
> >> it
> >>> for docking purpose my computer is freezing. Now how can I reduce my
> pdb
> >>> file size  from GB to MB for using it properly. please help me to deal
> >>> with this problem.
> >>> --
> >>> Gromacs Users mailing list
> >>>
> >>> * Please search the archive at
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Re: [gmx-users] (no subject)

[Chalaoux, Francois-Regis]

What is your protein, PDB Id ?

FR.

> Le 14 mai 2016 à 12:04:09, Upasana Ray  a écrit :
> 
> yes I have removed water & the pdb file only contains  protein
> 
> On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
> francois-regis.chala...@evotec.com> wrote:
> 
>> Hi,
>> 
>> Did you removed Water ?
>> Check also there is no other protein in the same file.
>> 
>> FR.
>> 
>>> Le 14 mai 2016 à 07:04:15, Upasana Ray  a
>> écrit :
>>> 
>>> Dear  user,
>>> 
>>> I have generated my final protein.pdb file by using trjconv command from
>>> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening
>> it
>>> for docking purpose my computer is freezing. Now how can I reduce my pdb
>>> file size  from GB to MB for using it properly. please help me to deal
>>> with this problem.
>>> --
>>> 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] (no subject)

[Upasana Ray]

yes I have removed water & the pdb file only contains  protein

On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis <
francois-regis.chala...@evotec.com> wrote:

> Hi,
>
> Did you removed Water ?
> Check also there is no other protein in the same file.
>
> FR.
>
> > Le 14 mai 2016 à 07:04:15, Upasana Ray  a
> écrit :
> >
> > Dear  user,
> >
> > I have generated my final protein.pdb file by using trjconv command from
> > .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening
> it
> > for docking purpose my computer is freezing. Now how can I reduce my pdb
> > file size  from GB to MB for using it properly. please help me to deal
> > with this problem.
> > --
> > 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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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

[Justin Lemkul]

On 5/14/16 3:48 AM, Husen R wrote:

Hi,

Currently I'm running this tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html)
to simulate restart with fewer nodes.
at restart, I changed the amount of nodes from 3 to 2 nodes.
I also changed the amount of processes from 24 to 16 processes.

While the application is running, I tried to see the output file.
This is the content of the output file :

#output file


Reading checkpoint file md_0_1.cpt generated: Sat May 14 13:10:25 2016

  #ranks mismatch,
current program: 16
checkpoint file: 24

  #PME-ranks mismatch,
current program: -1
checkpoint file: 6

GROMACS patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.

Using 16 MPI processes
Using 1 OpenMP thread per MPI process

starting mdrun 'LYSOZYME in water'
50 steps,   1000.0 ps (continuing from step 54500,109.0 ps).



I got a mismatch note as described in the output file above. it is not a
problem, isn't it ?
I just want to make sure.



This is the message I mentioned in my first reply.  It just means you're now 
changing the DD configuration, PME nodes, etc. so it's not binary identical, but 
the state is faithfully preserved.


http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation


is it not allowed to use a different user when we restart simulation from
checkpoint file ?
Previously, I failed to restart simulation based on checkpoint file. I
guess, it is failed because I used a different user (Only a guess).


Presumably one just needs correct read/write permissions, though I have never 
tried to switch users when doing a continuation.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] simulation_time

[Justin Lemkul]

On 5/14/16 2:25 AM, Ms. Nikita Bora wrote:

Respected Sir,

Recently i followed your tutorial for simulation of a 50 ns final mdrun of
protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used. The
simulation runned at aorund 10 ns/day . While for the same  complex when
rvdw=rcoulomb=1 is made the run was 10 ns/day.

Sir i would like to know is there any standard value for rvdw,rcoulomb and
why a longer time is taken for 1.4 value



Longer cutoffs = more interactions to compute.

Cutoffs are part of the force field.  Don't change them from prescribed values 
without very strong justification.


-Justin



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==

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Ruth L. Kirschstein NRSA Postdoctoral Fellow

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

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

==
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Re: [gmx-users] (no subject)

[Chalaoux, Francois-Regis]

Hi, 

Did you removed Water ?
Check also there is no other protein in the same file.

FR.

> Le 14 mai 2016 à 07:04:15, Upasana Ray  a écrit :
> 
> Dear  user,
> 
> I have generated my final protein.pdb file by using trjconv command from
> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening it
> for docking purpose my computer is freezing. Now how can I reduce my pdb
> file size  from GB to MB for using it properly. please help me to deal
> with this problem.
> -- 
> 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] Restart simulation from checkpoint file with fewer nodes

[Husen R]

Hi,

Currently I'm running this tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html)
to simulate restart with fewer nodes.
at restart, I changed the amount of nodes from 3 to 2 nodes.
I also changed the amount of processes from 24 to 16 processes.

While the application is running, I tried to see the output file.
This is the content of the output file :

#output file


Reading checkpoint file md_0_1.cpt generated: Sat May 14 13:10:25 2016

  #ranks mismatch,
current program: 16
checkpoint file: 24

  #PME-ranks mismatch,
current program: -1
checkpoint file: 6

GROMACS patchlevel, binary or parallel settings differ from previous run.
Continuation is exact, but not guaranteed to be binary identical.

Using 16 MPI processes
Using 1 OpenMP thread per MPI process

starting mdrun 'LYSOZYME in water'
50 steps,   1000.0 ps (continuing from step 54500,109.0 ps).



I got a mismatch note as described in the output file above. it is not a
problem, isn't it ?
I just want to make sure.

is it not allowed to use a different user when we restart simulation from
checkpoint file ?
Previously, I failed to restart simulation based on checkpoint file. I
guess, it is failed because I used a different user (Only a guess).
Thank you in advance.

regards,

Husen




On Sat, May 14, 2016 at 7:58 AM, Justin Lemkul  wrote:

>
>
> On 5/13/16 8:53 PM, Husen R wrote:
>
>> Dear all
>>
>> Does simulation able to be restarted from checkpoint file with fewer
>> nodes ?
>> let's say, at the first time, I run simulation with 3 nodes. At running
>> time, one of those nodes is crashed and the simulation is terminated.
>>
>> I want to restart that simulation immadiately based on checkpoint file
>> with
>> the remaining 2 nodes. does gromacs support such case ?
>> I need help.
>>
>
> Have you tried it?  It should work.  You will probably get a note about
> the continuation not being exact due to a change in the number of cores,
> but the run should proceed fine.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] simulation_time

[Ms. Nikita Bora]

Respected Sir,

Recently i followed your tutorial for simulation of a 50 ns final mdrun of
protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used. The
simulation runned at aorund 10 ns/day . While for the same  complex when
rvdw=rcoulomb=1 is made the run was 10 ns/day.

Sir i would like to know is there any standard value for rvdw,rcoulomb and
why a longer time is taken for 1.4 value


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Re: [gmx-users] (no subject)

[Tsjerk Wassenaar]

Hi Upasana,

What is your goal, your research objective? 'opening it for docking
purpose' is way too vague for us to help you, other then suggesting that
you are probably not choosing an optimal approach.

Cheers,

Tsjerk
On May 14, 2016 07:04, "Upasana Ray"  wrote:

> Dear  user,
>
>  I have generated my final protein.pdb file by using trjconv command from
> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening it
> for docking purpose my computer is freezing. Now how can I reduce my pdb
> file size  from GB to MB for using it properly. please help me to deal
>  with this problem.
> --
> 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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> 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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