[gmx-users] How to calculate the MSD of center of mass of molecules

[Zheng Gong]

Hello everyone,

In my simulation, I want to calculate the MSD of COM of some molecules
using *gmx msd* command.

>From the Gromacs manual, *For molecules consisting of more than one atom,
ri can be taken as the center of mass positions of the molecules. In that
case, you should use an index file with molecule numbers.*

It seems that all i need to do is create an index file with molecule
numbers. Following is my procedure:


*echo 'res_com of resname Tf2N' | gmx select -s nvt-msd.tpr -on mol.ndx*

*gmx msd -f nvt-msd.xtc -s nvt-msd.tpr -n mol.ndx -o msd-com*

However, it does not produce the result what I want. The resulting
msd-com.xvg is not the MSD of COM of Tf2N molecule. It seems that mol.ndx
has not been recognize  as molecule numbers.

Is there anything I missed?

-- 
Gong, Zheng
Doctoral Candidate in Physical Chemistry
School of Chemistry and Chemical Engineering
Shanghai Jiao Tong University
http://sun.sjtu.edu.cn
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[gmx-users] Area per lipid through the time lipid membranes and mixed membranes

[Poncho Arvayo Zatarain]

Hello gromacs user: I obtained the average area per lipid for dppc and dppe 
membrane, also for mixed membranes of dppc/dppe/embedded molecule. But i want 
to obtain the diagram of the area per lipid through the time, the course of my 
simulation for my dppc, dppe membranes and mixed membranes with a molecule 
inside. Is there any command in gromacs or what should i do?

Thanks
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Re: [gmx-users] Box size problem

[Justin Lemkul]

On 3/15/17 3:09 PM, Davit Hakobyan wrote:

Dear All,

I try to run a simulation with protein-membrane system in charmm36 ff with
Gromacs5.0.4 and the simulation runs without complain.The problem is in the unit
cell size which seems to grow during a short 500 ps simulation from ~15 to ~28
nm in Z direction although the system atoms remain confined in the~15 nm in Z
direction.


The GRO files before and after the 500 ps simulation can be downloaded from the
following link: https://uni-muenster.sciebo.de/index.php/s/GBHjED2t1KzZZ2o



Your initial coordinates are badly fragmented, with regions of vacuum and 
isolated water molecules.  You're going to get bizarre behavior as the system 
collapses to try to close those voids.  This outcome likely isn't a function of 
.mdp settings, but unphysical initial coordinates.




Bonus comments!


MDP Parameters (OLD)
-
integrator  = md
dt  = 0.002
nsteps  = 25000

nstxout = 50
nstvout = 50
nstlog  = 10
nstenergy   = 50
nstxtcout   = 50
xtc_grps=

energygrps  = Protein CHL1 POPC DOPC POPS Water_and_ions
;energygrp_table=
nstcalcenergy   = 500
nstlist = 10
nstcomm = 50
comm_mode   = Linear
comm-grps   =
ns_type = grid
rlist   = 1.0
rlistlong   = 1.4
rvdw_switch = 0.8
vdwtype = Switch


This is a potential switch, not a force switch, so lipid simulations done with 
these settings will have artificial behavior.  Force switching is standard for 
all CHARMM additive force field simulations, and is absolutely required for lipids.



coulombtype = pme
rcoulomb= 1.0
rcoulomb_switch = 0.0
rvdw= 1.2
fourierspacing  = 0.15
pme_order   = 6
;ewald_rtol = 1e-6
tcoupl  = V-rescale ;nose-hoover
nhchainlength   = 1
tc-grps = Protein CHL1 POPC DOPC POPS Water_and_ions


Coupling all different types of molecules in the system to their own thermostats 
is inappropriate.


-Justin


tau_t   = 0.1 0.1 0.1 0.1 0.1 0.1
ref_t   = 293 293 293 293 293 293
Pcoupl  = parrinello-rahman ;berendsen ;parrinello-rahman
Pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p   = 1.0 1.0
pbc = xyz
gen_vel = no ;yes
gen_temp= 293
optimize_fft= yes
constraints = hbonds
continuation= no
constraint_algorithm = Lincs
lincs-order = 4 ; 8 is needed for BD with large time-steps.
lincs-iter  = 1 ; 1 is fine for normal simulations, but use 2 to
conserve energy in NVE runs.
-

In the new parameters I also tried to change the tcoupl from Nose-Hoover to
V-rescale, but the outcome is the same, the box size becomes large.

ProbablyI am missing something trivial.
Does anybody have a clue what might be wrong?

Thanks very much for any help.
Davit


--
==

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] Problem with combining the .edr files

[Mohsen Ramezanpour]

Thanks Mark :-)
Problem solved.



On Wed, Mar 15, 2017 at 1:10 PM, Mark Abraham 
wrote:

> Hi,
>
> Judging from your start times, you're concatenating apples with oranges :-)
> In this case, probably NVT equilibration with NPT production, or similar.
> Arguably, concatenating the trr files in that case is also conceptually
> wrong, even if the file format is not robust enough to hint that you're
> trying to do something that will leave you with a file whose contents have
> an interpretation that is somewhere between unclear and wrong. edr is
> actually smart enough to perhaps stop you doing something that isn't
> useful.
>
> Mark
>
> On Wed, Mar 15, 2017 at 7:26 PM Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I did a simulation in parts using -noappend command, so I have a few .trr
> > and .edr files which I wish to merge.
> >
> > I have difficulty with that and I could not find any related post on that
> > except this one:
> > http://comments.gmane.org/gmane.science.biology.gromacs.user/68806
> >
> > Using Gromacs 2016.2 installed on my PC (without MPI), and the following
> > command:
> > gmx trjcat -f *.trr  -o  fixed.trr
> > I will have a reasonable .trr file. However, when I use:
> >
> > gmx eneconv -f *.edr  -o  fixed.edr
> >
> > I get the followings:
> > 
> > Opened NJOB_1.edr as single precision energy file
> > Last energy frame read 0 time0.000
> > Opened NJOB_2.edr as single precision energy file
> > Energy files don't match, different number of energies:
> >  NJOB_1.edr: 55
> >  NJOB_2.edr: 55
> >
> > Continue conversion using only the first 55 terms (n/y)?
> > (you should be sure that the energy terms match)
> > y
> > Reading energy frame  0 time0.000
> > Opened NJOB_3.edr as single precision energy file
> > Energy files don't match, different number of energies:
> >  NJOB_2.edr: 55
> >  NJOB_3.edr: 58
> >
> > Continue conversion using only the first 55 terms (n/y)?
> > (you should be sure that the energy terms match)
> > y
> > Reading energy frame  0 time0.000
> > Opened NJOB_4.edr as single precision energy file
> > Energy files don't match, different number of energies:
> >  NJOB_3.edr: 58
> >  NJOB_4.edr: 57
> >
> > Continue conversion using only the first 55 terms (n/y)?
> > (you should be sure that the energy terms match)
> > y
> > Reading energy frame  0 time 4.000
> > Opened NJOB_5.edr as single precision energy file
> > Energy files don't match, different number of energies:
> >  NJOB_4.edr: 57
> >  NJOB_5.edr: 60
> >
> > Continue conversion using only the first 55 terms (n/y)?
> > (you should be sure that the energy terms match)
> > y
> > Reading energy frame  0 time 8.000
> > Opened system_MD.5.edr.edr as single precision energy file
> > Reading energy frame  0 time 12.000
> > Opened system_MD.5.part0003.edr.edr as single precision energy file
> > Reading energy frame  0 time 32.000
> > Opened system_MD.5.part0004.edr.edr as single precision energy file
> > Reading energy frame  0 time 57.000
> > Opened system_MD.5.part0005.edr.edr as single precision energy file
> > Reading energy frame  0 time 82.000
> >
> > Summary of files and start times used:
> >
> >   FileStart time
> > -
> >NJOB_1.edr0.000
> >NJOB_2.edr0.000
> >NJOB_3.edr0.000
> >NJOB_4.edr4.000
> >NJOB_5.edr8.000
> >   system_MD.5.edr.edr   12.000
> > system_MD.5.part0003.edr.edr   32.000
> > system_MD.5.part0004.edr.edr   57.000
> > system_MD.5.part0005.edr.edr   82.000
> >
> > Opened NJOB_1.edr as single precision energy file
> > Reading energy frame  0 time0.000
> > Continue writing frames from t=0, step=0
> > Last energy frame read 0 time0.000
> > Last step written from NJOB_1.edr: t 0, step 0
> >
> > Opened NJOB_2.edr as single precision energy file
> > Reading energy frame  1 time2.500
> > Last step written from NJOB_2.edr: t 0, step 0
> >
> > Opened NJOB_3.edr as single precision energy file
> > Reading energy frame  1 time   20.000
> > Continue writing frames from t=20, step=1
> > Last energy frame read 2000 time 4.000 Writing frame time
> > 4
> > Last step written from NJOB_3.edr: t 4, step 2000
> >
> > Opened NJOB_4.edr as single precision energy file
> > Reading energy frame  1 time 40020.000
> > Continue writing frames from t=40020, step=2001
> > Last energy frame read 2000 time 8.000 Writing frame time
> > 8
> > Last step written from NJOB_4.edr: t 8, step 4000
> >
> > Opened NJOB_5.edr as single precision energy file
> > Reading energy frame  1 time 80020.000
> > Continue writing frames from t=80020, step=4001
> > Last energy frame read 

[gmx-users] Lipid head movement normal to monolayer.

[Merril Mathew]

Dear all,

I want to calculate how much my lipid heads emerse into water in a
monolayer after simulation. I want to compare the movement of the lipids
from the intial conformation to the final conformation. Is there a way to
calculate such movement using GROMACS?

Merril.
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Re: [gmx-users] Makeing movies using VMD

[Andrea Spitaleri]

Hi

have look to viewchange rendering and make movie options in vmd:

http://www.dxulab.com/wiki/vmdviewchangerenderingtutorial


On 15/03/2017 18:16, Mark Abraham wrote:

Hi,

I suggest you have a look at the VMD website for their documentation.
THere's very likely something for this.

Mark

On Wed, Mar 15, 2017 at 6:14 PM Poncho Arvayo Zatarain <
poncho_8...@hotmail.com> wrote:



Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1.
I finished my simulation and i have my tpr, xtc file, etc. How can i do the
movie using vmd and algo save it and attach it for paste it in a
powerpoint? I only can watch the trajectory in vmd, vut not save it and put
it on a powerpoint. Do i need to use another program?

Thanks
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--
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/-0003-3012-3557

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Re: [gmx-users] Problem with combining the .edr files

[Mark Abraham]

Hi,

Judging from your start times, you're concatenating apples with oranges :-)
In this case, probably NVT equilibration with NPT production, or similar.
Arguably, concatenating the trr files in that case is also conceptually
wrong, even if the file format is not robust enough to hint that you're
trying to do something that will leave you with a file whose contents have
an interpretation that is somewhere between unclear and wrong. edr is
actually smart enough to perhaps stop you doing something that isn't useful.

Mark

On Wed, Mar 15, 2017 at 7:26 PM Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear Gromacs users,
>
> I did a simulation in parts using -noappend command, so I have a few .trr
> and .edr files which I wish to merge.
>
> I have difficulty with that and I could not find any related post on that
> except this one:
> http://comments.gmane.org/gmane.science.biology.gromacs.user/68806
>
> Using Gromacs 2016.2 installed on my PC (without MPI), and the following
> command:
> gmx trjcat -f *.trr  -o  fixed.trr
> I will have a reasonable .trr file. However, when I use:
>
> gmx eneconv -f *.edr  -o  fixed.edr
>
> I get the followings:
> 
> Opened NJOB_1.edr as single precision energy file
> Last energy frame read 0 time0.000
> Opened NJOB_2.edr as single precision energy file
> Energy files don't match, different number of energies:
>  NJOB_1.edr: 55
>  NJOB_2.edr: 55
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame  0 time0.000
> Opened NJOB_3.edr as single precision energy file
> Energy files don't match, different number of energies:
>  NJOB_2.edr: 55
>  NJOB_3.edr: 58
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame  0 time0.000
> Opened NJOB_4.edr as single precision energy file
> Energy files don't match, different number of energies:
>  NJOB_3.edr: 58
>  NJOB_4.edr: 57
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame  0 time 4.000
> Opened NJOB_5.edr as single precision energy file
> Energy files don't match, different number of energies:
>  NJOB_4.edr: 57
>  NJOB_5.edr: 60
>
> Continue conversion using only the first 55 terms (n/y)?
> (you should be sure that the energy terms match)
> y
> Reading energy frame  0 time 8.000
> Opened system_MD.5.edr.edr as single precision energy file
> Reading energy frame  0 time 12.000
> Opened system_MD.5.part0003.edr.edr as single precision energy file
> Reading energy frame  0 time 32.000
> Opened system_MD.5.part0004.edr.edr as single precision energy file
> Reading energy frame  0 time 57.000
> Opened system_MD.5.part0005.edr.edr as single precision energy file
> Reading energy frame  0 time 82.000
>
> Summary of files and start times used:
>
>   FileStart time
> -
>NJOB_1.edr0.000
>NJOB_2.edr0.000
>NJOB_3.edr0.000
>NJOB_4.edr4.000
>NJOB_5.edr8.000
>   system_MD.5.edr.edr   12.000
> system_MD.5.part0003.edr.edr   32.000
> system_MD.5.part0004.edr.edr   57.000
> system_MD.5.part0005.edr.edr   82.000
>
> Opened NJOB_1.edr as single precision energy file
> Reading energy frame  0 time0.000
> Continue writing frames from t=0, step=0
> Last energy frame read 0 time0.000
> Last step written from NJOB_1.edr: t 0, step 0
>
> Opened NJOB_2.edr as single precision energy file
> Reading energy frame  1 time2.500
> Last step written from NJOB_2.edr: t 0, step 0
>
> Opened NJOB_3.edr as single precision energy file
> Reading energy frame  1 time   20.000
> Continue writing frames from t=20, step=1
> Last energy frame read 2000 time 4.000 Writing frame time
> 4
> Last step written from NJOB_3.edr: t 4, step 2000
>
> Opened NJOB_4.edr as single precision energy file
> Reading energy frame  1 time 40020.000
> Continue writing frames from t=40020, step=2001
> Last energy frame read 2000 time 8.000 Writing frame time
> 8
> Last step written from NJOB_4.edr: t 8, step 4000
>
> Opened NJOB_5.edr as single precision energy file
> Reading energy frame  1 time 80020.000
> Continue writing frames from t=80020, step=4001
> Last energy frame read 2000 time 12.000 Writing frame time
> 12
> Last step written from NJOB_5.edr: t 12, step 6000
>
> Opened system_MD.5.edr.edr as single precision energy file
> Reading energy frame  1 time 120020.000
> Continue writing frames from t=120020, step=6001
> Last energy frame read 1 time 32.000 riting frame time
> 

[gmx-users] Box size problem

[Davit Hakobyan]

Dear All,

I try to run a simulation with protein-membrane system in charmm36 ff 
with Gromacs5.0.4 and the simulation runs without complain.The problem 
is in the unit cell size which seems to grow during a short 500 ps 
simulation from ~15 to ~28 nm in Z direction although the system atoms 
remain confined in the~15 nm in Z direction.



The GRO files before and after the 500 ps simulation can be downloaded 
from the following link: 
https://uni-muenster.sciebo.de/index.php/s/GBHjED2t1KzZZ2o


And these are the MDP parameters used:

MDP Parameters
-
integrator = md
dt  = 0.001
nsteps  = 50

nstxout = 50
nstvout = 50
nstlog  = 10
nstenergy   = 50
nstxtcout   = 50
xtc_grps=
nstcalcenergy   = 500

energygrps  = ANA2 CHL1 POPC DOPC POPI POPS CAL

cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
coulombtype = pme
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
;
tcoupl  = Nose-Hoover
tc_grps = PROT   MEMB   SOL_ION
tau_t   = 1.01.01.0
;ref_t   = 303.15 303.15 303.15
ref_t   = 200. 200. 200.
;
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5  4.5e-5
ref_p   = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = PROT   MEMB   SOL_ION
;
refcoord_scaling= com
-

No evident problem was displayed at TPRpreparation or MD run.


Could some combination of parameters cause such a problem?
With Gromacs 5.0.4 I have successfully simulated similar 
protein-membrane systemsin the past with the same charmm36 force field, 
but at that time different parameters I remember were suggested in 
Gromacs, particularly, the following ones:


MDP Parameters (OLD)
-
integrator  = md
dt  = 0.002
nsteps  = 25000

nstxout = 50
nstvout = 50
nstlog  = 10
nstenergy   = 50
nstxtcout   = 50
xtc_grps=

energygrps  = Protein CHL1 POPC DOPC POPS Water_and_ions
;energygrp_table=
nstcalcenergy   = 500
nstlist = 10
nstcomm = 50
comm_mode   = Linear
comm-grps   =
ns_type = grid
rlist   = 1.0
rlistlong   = 1.4
rvdw_switch = 0.8
vdwtype = Switch
coulombtype = pme
rcoulomb= 1.0
rcoulomb_switch = 0.0
rvdw= 1.2
fourierspacing  = 0.15
pme_order   = 6
;ewald_rtol = 1e-6
tcoupl  = V-rescale ;nose-hoover
nhchainlength   = 1
tc-grps = Protein CHL1 POPC DOPC POPS Water_and_ions
tau_t   = 0.1 0.1 0.1 0.1 0.1 0.1
ref_t   = 293 293 293 293 293 293
Pcoupl  = parrinello-rahman ;berendsen ;parrinello-rahman
Pcoupltype  = semiisotropic
tau_p   = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p   = 1.0 1.0
pbc = xyz
gen_vel = no ;yes
gen_temp= 293
optimize_fft= yes
constraints = hbonds
continuation= no
constraint_algorithm = Lincs
lincs-order = 4 ; 8 is needed for BD with large time-steps.
lincs-iter  = 1 ; 1 is fine for normal simulations, but use 2 to 
conserve energy in NVE runs.

-

In the new parameters I also tried to change the tcoupl from Nose-Hoover 
to V-rescale, but the outcome is the same, the box size becomes large.


ProbablyI am missing something trivial.
Does anybody have a clue what might be wrong?

Thanks very much for any help.
Davit
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[gmx-users] Problem with combining the .edr files

[Mohsen Ramezanpour]

Dear Gromacs users,

I did a simulation in parts using -noappend command, so I have a few .trr
and .edr files which I wish to merge.

I have difficulty with that and I could not find any related post on that
except this one:
http://comments.gmane.org/gmane.science.biology.gromacs.user/68806

Using Gromacs 2016.2 installed on my PC (without MPI), and the following
command:
gmx trjcat -f *.trr  -o  fixed.trr
I will have a reasonable .trr file. However, when I use:

gmx eneconv -f *.edr  -o  fixed.edr

I get the followings:

Opened NJOB_1.edr as single precision energy file
Last energy frame read 0 time0.000
Opened NJOB_2.edr as single precision energy file
Energy files don't match, different number of energies:
 NJOB_1.edr: 55
 NJOB_2.edr: 55

Continue conversion using only the first 55 terms (n/y)?
(you should be sure that the energy terms match)
y
Reading energy frame  0 time0.000
Opened NJOB_3.edr as single precision energy file
Energy files don't match, different number of energies:
 NJOB_2.edr: 55
 NJOB_3.edr: 58

Continue conversion using only the first 55 terms (n/y)?
(you should be sure that the energy terms match)
y
Reading energy frame  0 time0.000
Opened NJOB_4.edr as single precision energy file
Energy files don't match, different number of energies:
 NJOB_3.edr: 58
 NJOB_4.edr: 57

Continue conversion using only the first 55 terms (n/y)?
(you should be sure that the energy terms match)
y
Reading energy frame  0 time 4.000
Opened NJOB_5.edr as single precision energy file
Energy files don't match, different number of energies:
 NJOB_4.edr: 57
 NJOB_5.edr: 60

Continue conversion using only the first 55 terms (n/y)?
(you should be sure that the energy terms match)
y
Reading energy frame  0 time 8.000
Opened system_MD.5.edr.edr as single precision energy file
Reading energy frame  0 time 12.000
Opened system_MD.5.part0003.edr.edr as single precision energy file
Reading energy frame  0 time 32.000
Opened system_MD.5.part0004.edr.edr as single precision energy file
Reading energy frame  0 time 57.000
Opened system_MD.5.part0005.edr.edr as single precision energy file
Reading energy frame  0 time 82.000

Summary of files and start times used:

  FileStart time
-
   NJOB_1.edr0.000
   NJOB_2.edr0.000
   NJOB_3.edr0.000
   NJOB_4.edr4.000
   NJOB_5.edr8.000
  system_MD.5.edr.edr   12.000
system_MD.5.part0003.edr.edr   32.000
system_MD.5.part0004.edr.edr   57.000
system_MD.5.part0005.edr.edr   82.000

Opened NJOB_1.edr as single precision energy file
Reading energy frame  0 time0.000
Continue writing frames from t=0, step=0
Last energy frame read 0 time0.000
Last step written from NJOB_1.edr: t 0, step 0

Opened NJOB_2.edr as single precision energy file
Reading energy frame  1 time2.500
Last step written from NJOB_2.edr: t 0, step 0

Opened NJOB_3.edr as single precision energy file
Reading energy frame  1 time   20.000
Continue writing frames from t=20, step=1
Last energy frame read 2000 time 4.000 Writing frame time
4
Last step written from NJOB_3.edr: t 4, step 2000

Opened NJOB_4.edr as single precision energy file
Reading energy frame  1 time 40020.000
Continue writing frames from t=40020, step=2001
Last energy frame read 2000 time 8.000 Writing frame time
8
Last step written from NJOB_4.edr: t 8, step 4000

Opened NJOB_5.edr as single precision energy file
Reading energy frame  1 time 80020.000
Continue writing frames from t=80020, step=4001
Last energy frame read 2000 time 12.000 Writing frame time
12
Last step written from NJOB_5.edr: t 12, step 6000

Opened system_MD.5.edr.edr as single precision energy file
Reading energy frame  1 time 120020.000
Continue writing frames from t=120020, step=6001
Last energy frame read 1 time 32.000 riting frame time
32
Last step written from system_MD.5.edr.edr: t 32, step 16000

Opened system_MD.5.part0003.edr.edr as single precision energy file
Reading energy frame  1 time 320020.000
Continue writing frames from t=320020, step=16001
Last energy frame read 12500 time 57.000 riting frame time
56
Last step written from system_MD.5.part0003.edr.edr: t 57, step
28500

Opened system_MD.5.part0004.edr.edr as single precision energy file
Reading energy frame  1 time 570020.000
Continue writing frames from t=570020, step=28501
Last energy frame read 12500 time 82.000 riting frame time
82
Last step written from system_MD.5.part0004.edr.edr: t 82, step
41000

Opened system_MD.5.part0005.edr.edr as single precision energy file
Reading energy frame  1 time 

Re: [gmx-users] EM did not converge crashing drude system

[Justin Lemkul]

On 3/15/17 1:19 PM, Dayhoff, Guy wrote:

I have a drude system that I have minimized, and equilibrated through nvt
and npt ensembles using position restraints (all with scf). As I perform the
production runs i’m facing random crashes that seem to be related to EM
did not converge messages. This has happened anywhere from tens of
thousands of steps in, to millions of steps in. Below is an example and
the mdp options for the run.



Please contact me off-list about this.  These are not officially supported 
features and there are possibly bugs but I will need better descriptions of what 
you're doing and all your input files.


-Justin



My Best,
   Guy Dayhoff

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

step 393698: EM did not converge in 20 iterations, RMS force 15.668
step 393699: EM did not converge in 20 iterations, RMS force 88.569
step 393700: EM did not converge in 20 iterations, RMS force 341.002
step 393701: EM did not converge in 20 iterations, RMS force 680.888
step 393702: EM did not converge in 20 iterations, RMS force 1147.229
step 393703: EM did not converge in 20 iterations, RMS force 1077.486


=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
MDP options:

; RUN CONTROL
integrator   = md
nsteps   = 5000 ;50ns
dt   = 0.001

; OUTPUT CONTROL
nstxout  = 0
nstvout  = 1 ;every 10ps for now
nstfout  = 1
nstlog   = 1
nstenergy= 1
nstcalcenergy= 1
nstxout-compressed   = 1
compressed-x-grps= System

; NEIGHBOR SEARCHING
cutoff-scheme= verlet
nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 1.2

; BONDS
constraints  = h-bonds
continuation = yes

; ELECTROSTATICS AND VdW
coulombtype  = PME
rcoulomb = 1.2
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
DispCorr = EnerPres

; EWALD
pme_order= 4
fourierspacing   = 0.16

; TEMPERATURE COUPLING
Tcoupl   = Nose-Hoover
tc-grps  = Water non-Water
tau_t= 10.0 10.0
ref_t= 300 300
nh-chain-length  = 1

; VELOCITY GENERATION
gen-vel  = no

; PRESSURE COUPLING
Pcoupl   = Parrinello-Rahman
Pcoupltype   = semiisotropic
tau_p= 50.0
compressibility  = 4.5e-5 4.5e-5
ref_p= 0.0 3.0

; DRUDE POLARIZATION
drude   = yes
drude-mode  = SCF
drude-hyper = yes
drude-khyp  = 16736000.0
drude-r = 0.02
drude-pow   = 4



--
==

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] EM did not converge crashing drude system

[Dayhoff, Guy]

I have a drude system that I have minimized, and equilibrated through nvt 
and npt ensembles using position restraints (all with scf). As I perform the
production runs i’m facing random crashes that seem to be related to EM
did not converge messages. This has happened anywhere from tens of
thousands of steps in, to millions of steps in. Below is an example and
the mdp options for the run.


My Best,
   Guy Dayhoff

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

step 393698: EM did not converge in 20 iterations, RMS force 15.668
step 393699: EM did not converge in 20 iterations, RMS force 88.569
step 393700: EM did not converge in 20 iterations, RMS force 341.002
step 393701: EM did not converge in 20 iterations, RMS force 680.888
step 393702: EM did not converge in 20 iterations, RMS force 1147.229
step 393703: EM did not converge in 20 iterations, RMS force 1077.486


=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
MDP options:

; RUN CONTROL
integrator   = md
nsteps   = 5000 ;50ns
dt   = 0.001

; OUTPUT CONTROL
nstxout  = 0
nstvout  = 1 ;every 10ps for now
nstfout  = 1
nstlog   = 1
nstenergy= 1
nstcalcenergy= 1
nstxout-compressed   = 1
compressed-x-grps= System

; NEIGHBOR SEARCHING
cutoff-scheme= verlet
nstlist  = 10 
ns-type  = Grid
pbc  = xyz
rlist= 1.2

; BONDS
constraints  = h-bonds
continuation = yes

; ELECTROSTATICS AND VdW
coulombtype  = PME
rcoulomb = 1.2
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
DispCorr = EnerPres

; EWALD
pme_order= 4
fourierspacing   = 0.16

; TEMPERATURE COUPLING
Tcoupl   = Nose-Hoover
tc-grps  = Water non-Water
tau_t= 10.0 10.0
ref_t= 300 300
nh-chain-length  = 1

; VELOCITY GENERATION
gen-vel  = no

; PRESSURE COUPLING
Pcoupl   = Parrinello-Rahman
Pcoupltype   = semiisotropic
tau_p= 50.0
compressibility  = 4.5e-5 4.5e-5
ref_p= 0.0 3.0

; DRUDE POLARIZATION
drude   = yes
drude-mode  = SCF
drude-hyper = yes
drude-khyp  = 16736000.0
drude-r = 0.02
drude-pow   = 4

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Re: [gmx-users] Makeing movies using VMD

[Mark Abraham]

Hi,

I suggest you have a look at the VMD website for their documentation.
THere's very likely something for this.

Mark

On Wed, Mar 15, 2017 at 6:14 PM Poncho Arvayo Zatarain <
poncho_8...@hotmail.com> wrote:

>
>
> Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1.
> I finished my simulation and i have my tpr, xtc file, etc. How can i do the
> movie using vmd and algo save it and attach it for paste it in a
> powerpoint? I only can watch the trajectory in vmd, vut not save it and put
> it on a powerpoint. Do i need to use another program?
>
> Thanks
> --
> 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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[gmx-users] Makeing movies using VMD

[Poncho Arvayo Zatarain]

Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1. I 
finished my simulation and i have my tpr, xtc file, etc. How can i do the movie 
using vmd and algo save it and attach it for paste it in a powerpoint? I only 
can watch the trajectory in vmd, vut not save it and put it on a powerpoint. Do 
i need to use another program?

Thanks
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Re: [gmx-users] Computational electrophysiology, implicit solvent and coarse-grained system: atom/molecule definitions?

[Kutzner, Carsten]

Hi,

> On 14 Mar 2017, at 11:18, Vries, de, H.W.  
> wrote:
> 
> Dear all,
> 
> I am currently trying to run the computational electrophysiology scheme on
> an implicit solvent, coarse-grained system by introducing a little
> workaround:
> 
> In the manual, it is stated that we can tell the routine what molecules are
> 'solvent', and what molecules are 'ions' through custom index groups. As my
> system thus does not have water molecules, I inserted non-interacting dummy
> particles into the system, which I then tell the CompEl scheme to use as a
> solvent group for swapping (via custom index groups)
> 
> However, the simulation gets stuck at:
> 
> SWAP: Making sure each atom belongs to at most one of the swap groups.
> SWAP: Checking whether all ion molecules consist of 20012 atoms
> SWAP: Checking whether all solvent molecules consist of 20012 atoms
> SWAP: Opening output file swapions.xvg
> SWAP: Determining initial ion counts.
How does your topol.top file look like? It should list the correct
number of copies of each ion / molecule.

Is this the most recent version (2016)?

Best,
  Carsten

> 
> Looking at swapions.xvg, I see that the routine doesn't recognize my
> coarse-grained atoms correctly: 4800,7206 and 800 are the correct numbers
> of coarse-grained atoms that I put in, with 20012 being the total number of
> coarse-grained beads that I have in my system:
> 
> # ion group contains 4800 atoms with 20012 atoms in each molecule.
> # split0 group contains 7206 atoms.
> # split1 group contains 7206 atoms.
> # solvent group contains 800 atoms with 20012 atoms in each molecule.
> 
> Can anyone give me a pointer as to what might be going wrong (I can send
> the files directly if requested)? Could this be an issue with the
> coarse-grained model im employing, that it is not defined properly in my
> topology, or is CompEl really incompatible with any implicit solvent
> CG-representation that tries to use dummy particles for swapping purposes?
> 
> 
> Thank you kindly,
> 
> Henry de Vries
> 
> -- 
> Henry de Vries
> Student Topmaster Nanoscience
> Micromechanics of Materials Group
> tel: +31 (0)6-30520328
> office: X5113.0129
> Nijenborgh 4, 9747AG
> Groningen, Netherlands
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Re: [gmx-users] Gromacs installation on GPU

[Mark Abraham]

Hi,

The more simple way to cater for all possibilities is to configure with GPU
support the first time. mdrun observes whether there are actually GPUs at
run time and executes accordingly. But as Justin says, this requires that
you install CUDA when you might not use it, which is usually more
inconvenient than a second GROMACS install when you later decide you need
GPU support.

Mark

On Wed, Mar 15, 2017 at 1:55 PM Justin Lemkul  wrote:

>
>
> On 3/15/17 8:43 AM, Andrew Bostick wrote:
> > Dear Gromacs users,
> >
> > I had installed gromacs using following commands:
> >
> > tar xvf cmake-3.6.1.tar.gz
> > tar xvzf gromacs-5.1.3.tar.gz
> >
> > cd ../cmake-3.6.1.
> > ./configure
> > make
> > make install
> >
> > cd ../gromacs-5.1.3
> > mkdir build
> > cd build
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DGMX_MPI=ON -DGMX_GPU=OFF
> > make
> > make check
> > make install
> > source /usr/local/gromacs/bin/GMXRC
> >
> > -
> >
> > Now I want to do MD simulation on GPU.
> >
> > Should I do installation again? Isn't there a more simple way?
> >
>
> The install process requires information about the GPU compatibility of the
> hardware, libraries etc, so yes, if you used -DGMX_GPU=OFF then you need to
> install again (ideally with a current version of GROMACS, or at minimum the
> latest patch release in the 5.1 series, rather than an old version of the
> code).
>
> -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
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> * Please search the archive at
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> posting!
>
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>
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>
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Re: [gmx-users] Gromacs installation on GPU

[Justin Lemkul]

On 3/15/17 8:43 AM, Andrew Bostick wrote:

Dear Gromacs users,

I had installed gromacs using following commands:

tar xvf cmake-3.6.1.tar.gz
tar xvzf gromacs-5.1.3.tar.gz

cd ../cmake-3.6.1.
./configure
make
make install

cd ../gromacs-5.1.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_MPI=ON -DGMX_GPU=OFF
make
make check
make install
source /usr/local/gromacs/bin/GMXRC

-

Now I want to do MD simulation on GPU.

Should I do installation again? Isn't there a more simple way?



The install process requires information about the GPU compatibility of the 
hardware, libraries etc, so yes, if you used -DGMX_GPU=OFF then you need to 
install again (ideally with a current version of GROMACS, or at minimum the 
latest patch release in the 5.1 series, rather than an old version of the code).


-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] Distance restraints on two TYR OH groups so that they are together

[Justin Lemkul]

On 3/15/17 6:28 AM, Vytautas Rakeviius wrote:

Hello, I try to add distance restraints on two TYR OH groups so that they are 
together in the end like this:

[ distance_restraints ]
 195 281 1 1 1 0.2 0.22 0.24 1000
But it does not work at least over time frame I tested, they even go further 
away from each other.

Here I share my all files:MD_4AK0_test_pub.tar.bz2


That's not a valid link.

If you're trying to keep 2 oxygen atoms at a distance of 0.2 nm, that's well 
within the (likely) repulsive wall of the LJ potential, as well as being 
repulsive from the perspective of the electrostatics.  You'll either need a 
massive biasing force to keep them close, or develop a different way to keep 
them at such a distance.  Why are you imposing this bias, and at such a short 
distance?


-Justin


System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p 
topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in wrong 
way?

|
|
|
|   ||

   |

  |
|
|   |
MD_4AK0_test_pub.tar.bz2
 MediaFire is a simple to use free service that lets you put all your photos, 
documents, music, and video in a si...  |   |

  |

  |





--
==

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] POSRES for umbrella sampling

[Justin Lemkul]

On 3/15/17 6:19 AM, stellatof wrote:

Dear all,
I have a question regarding the use of "POSRES" in .
In the umbrella sampling tutorial it says that POSRES is used to keep one chain
as an immobile reference in the pulling procedure. What is the effect of POSRES?
Does it keep the molecule center of mass fix or does it restrain the positions
of atoms inside the molecules? According to the manual I tought the latter one,
but then I don't understand how this helps in having an immobile reference.


By applying a harmonic biasing potential to each non-hydrogen atom with an 
origin for that potential at the starting coordinates, the motion of each heavy 
atom is restricted.



What problem would one have if not using the POSRES?



In the tutorial's case, the strength of the many hydrogen bonds between the 
peptide chains would simply causing the entire assembly to be dragged across the 
simulation box rather than inducing dissociation of one peptide.  Larger biasing 
forces lead to distortion of the structure.  The use of restraints in the 
tutorial (and corresponding paper, please read it as technical aspects are 
explained in more detail with references to other amyloid papers that use 
similar approaches) is not necessarily applicable to other umbrella sampling 
studies.



In the simulations I performed, when I pull one molecule, the one I restrained
using POSRES keeps its center of mass stable and has only small changes in its
internal structure. Is it the expected behaviour?



Yes, but whether or not you need restraints is the larger question.  For 
instance, I see no reason to use the tutorial's approach for a protein-ligand 
complex, in which the interactions will be comparatively weak (and also require 
a different pull vector setup, anyway).


-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] Gromacs installation on GPU

[Andrew Bostick]

Dear Gromacs users,

I had installed gromacs using following commands:

tar xvf cmake-3.6.1.tar.gz
tar xvzf gromacs-5.1.3.tar.gz

cd ../cmake-3.6.1.
./configure
make
make install

cd ../gromacs-5.1.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_MPI=ON -DGMX_GPU=OFF
make
make check
make install
source /usr/local/gromacs/bin/GMXRC

-

Now I want to do MD simulation on GPU.

Should I do installation again? Isn't there a more simple way?

Best,
Andrew
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[gmx-users] Distance restraints on two TYR OH groups so that they are together

[Vytautas Rakeviius]

Hello, I try to add distance restraints on two TYR OH groups so that they are 
together in the end like this:

[ distance_restraints ]
 195 281 1 1 1 0.2 0.22 0.24 1000
But it does not work at least over time frame I tested, they even go further 
away from each other.

Here I share my all files:MD_4AK0_test_pub.tar.bz2
System is small and easy to run (gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p 
topol.top -o md_0_1.tpr && gmx mdrun -deffnm md_0_1)What I am doing in wrong 
way?
  
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MD_4AK0_test_pub.tar.bz2
 MediaFire is a simple to use free service that lets you put all your photos, 
documents, music, and video in a si...  |   |

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[gmx-users] POSRES for umbrella sampling

[stellatof]

Dear all,
I have a question regarding the use of "POSRES" in .
In the umbrella sampling tutorial it says that POSRES is used to keep 
one chain as an immobile reference in the pulling procedure. What is the 
effect of POSRES? Does it keep the molecule center of mass fix or does 
it restrain the positions of atoms inside the molecules? According to 
the manual I tought the latter one, but then I don't understand how this 
helps in having an immobile reference.

What problem would one have if not using the POSRES?

In the simulations I performed, when I pull one molecule, the one I 
restrained using POSRES keeps its center of mass stable and has only 
small changes in its internal structure. Is it the expected behaviour?


Thanks in advance and best regards,

Francesco


--
Francesco Stellato, PhD
I.N.F.N. - Rome 'Tor Vergata'
Tel: +39 06 7259 4284
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