Re: [gmx-users] Surface tension for water

[Iman Ahmadabadi]

Dear Dan,

As you can see in the images I sent to you, there is no error massage in
output files. The properties of the system such as pressure or temperature
is so high, that's why I've concluded that the system is crashed.

Sincerely,
Iman

On Wed, Aug 30, 2017 at 12:44 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Hi Dan,
>
> There is no error massage, It's just a crashing and stopping the
> simulation. The version is 4.6.0.
>
> Iman
>
> On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Dan,
>>
>> I have attached the NPT.mdp file in the following:
>>
>> title =  NPT equilibration
>> ; Run parameters
>> integrator = md
>> nsteps = 2000
>> dt= 0.001
>>
>> ; Output control
>> nstxout = 500
>> nstvout = 500
>> nstenergy = 500
>> nstlog = 500
>>
>> ; Bond parameters
>> continuation= no
>> constraint_algorithm= lincs
>> constraints= all-bonds
>> lincs_iter= 1
>> lincs_order= 4
>>
>> ; Neighborsearching
>> cutoff-scheme   = Verlet
>> ns_type= grid
>> nstlist= 20
>> rlist   = 2.0
>> rcoulomb= 2.0
>> rvdw= 2.0
>>
>> ; Electrostatics
>> coulombtype= PME
>> pme_order= 4
>> fourierspacing = 0.12
>>
>> ; Temperature coupling is on
>> tcoupl = V-rescale
>> tc-grps = system
>> tau_t = 0.1
>> ref_t = 298.15
>>
>> ; Pressure coupling is on
>> pcoupl= berendsen
>> pcoupltype= surface-tension
>> tau_p= 2.0  2.0
>> ref_p= 1440  1.0
>> compressibility = 4.46e-5  0
>> refcoord_scaling= com
>>
>> ; Periodic boundary conditions
>> pbc = xyz
>>
>> ; Dispersion correction
>> DispCorr = EnerPres
>>
>> ; Velocity generation
>> gen_vel = yes
>> lincs_warnangle = 90
>>
>>
>> Now I'm gonna using semiisotropic instead of surface tension like in the
>> following:
>> pcoupltyp   = semiisotropic
>> tau_p = 0.5
>> ref_p  = 1.0  1.0
>> compressibility = 4.46e-5  0
>>
>> Thank you for your help.
>> Sincerely,
>> Iman
>>
>> On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
>> imanahmadabad...@gmail.com> wrote:
>>
>>> Dear All Users,
>>>
>>> I'm calculating the surface tension of the water, my box contains almost
>>> 5000 water molecule in the middle of that. Through NVT equilibration, I got
>>> reasonable results for surface tension but when I use NPT for my system,
>>> the system crashes every time. The pressure coupling options are in the
>>> following:
>>>
>>> pcoupltyp = surface-tension
>>> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
>>> three values)
>>> ref_p  = 1440  1.0
>>> compressibility = 4.46e-5  0
>>>
>>> first ref-p value is 720*2 = 1440. 720 is the surface tension of water
>>> in 298.15.
>>>
>>> Now, I'm going to use semiisotropic for P-coupling:
>>>
>>> pcoupltyp   = semiisotropic
>>> tau_p = 0.5
>>> ref_p  = 1.0  1.0
>>> compressibility = 4.46e-5  0
>>>
>>> Could I have any recommendation about my problem with surface-tension
>>> pcoupltyp? Am I right with semiisotropic options?
>>>
>>>
>>> Respectfully,
>>> Iman Ahmadabadi
>>>
>>
>>
>>
>> --
>> Iman Ahmadabadi
>>
>> Sharif University of Technology, Tehran, Iran
>>
>> Department of Physics and Chemistry
>>
>> Phone: (+98) 9156125273
>>
>> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
>>
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
>



-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Phone: (+98) 9156125273

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hi,

I will download and install APBS and try again.

I have already tried pre-compiled version of g_mmpbsa from the link you
suggested.

Thanks

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Aug 30, 2017 at 10:38 AM, Nikhil Maroli  wrote:

> Hell,
>
> Download APBS and install it then use the binary package of g_mmpbsa. or
> see here:
>
> Pre-compiled executable program
>
> Pre-compiled program does not require any external library or GROMACS and
> APBS package. These programs are standalone and without any dependency.
> Download, extract and use it.
>
>
> http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[Nikhil Maroli]

Hell,

Download APBS and install it then use the binary package of g_mmpbsa. or
see here:

Pre-compiled executable program

Pre-compiled program does not require any external library or GROMACS and
APBS package. These programs are standalone and without any dependency.
Download, extract and use it.


http://rashmikumari.github.io/g_mmpbsa/Download-and-Installation.html
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[neha chaudhary]

Hello,

I have not installed APBS. I have compiled g_mmpbsa without APBS. Should I
compile it with APBS?

Best Regards,

*Neha*

Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,





On Wed, Aug 30, 2017 at 10:23 AM, Nikhil Maroli  wrote:

> Hi,
>
> The segmentation fault error during polar energy calculations is due to
> APBS. I don't know whether you installed it properly or not.
> --
> Gromacs Users mailing list
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Re: [gmx-users] Fwd: Segmentation fault (core dumped) in g_mmpbsa

[Nikhil Maroli]

Hi,

The segmentation fault error during polar energy calculations is due to
APBS. I don't know whether you installed it properly or not.
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[gmx-users] Pure repulsive LJ potential for OPLSAA

[Lei]

Hi, gmx users,
I am wondering how can I set up a pure repulsive or attractive LJ potential
in the OPLSAA force field. Since you need to set up the sigma and epsilon
instead of C6 or C12, the pure repulsive requires sigma to be infinity and
epsilon need to be 0. Is there a way to achieve pure repulsive LJ potential?
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Re: [gmx-users] Surface tension for water

[Dan Gil]

Iman,

You get the error message in the terminal if you are running it on your own
machine. If you are running on a supercomputer, the error messages will be
directed to a file. How do you know the simulation is crashing without the
software telling you? Please find the message (check all outputs), wherever
it might be, and share it with us. Otherwise I don't know what the problem
could be.

Dan

On Tue, Aug 29, 2017 at 4:14 PM, Iman Ahmadabadi  wrote:

> Hi Dan,
>
> There is no error massage, It's just a crashing and stopping the
> simulation. The version is 4.6.0.
>
> Iman
>
> On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com
> > wrote:
>
> > Dear Dan,
> >
> > I have attached the NPT.mdp file in the following:
> >
> > title =  NPT equilibration
> > ; Run parameters
> > integrator = md
> > nsteps = 2000
> > dt= 0.001
> >
> > ; Output control
> > nstxout = 500
> > nstvout = 500
> > nstenergy = 500
> > nstlog = 500
> >
> > ; Bond parameters
> > continuation= no
> > constraint_algorithm= lincs
> > constraints= all-bonds
> > lincs_iter= 1
> > lincs_order= 4
> >
> > ; Neighborsearching
> > cutoff-scheme   = Verlet
> > ns_type= grid
> > nstlist= 20
> > rlist   = 2.0
> > rcoulomb= 2.0
> > rvdw= 2.0
> >
> > ; Electrostatics
> > coulombtype= PME
> > pme_order= 4
> > fourierspacing = 0.12
> >
> > ; Temperature coupling is on
> > tcoupl = V-rescale
> > tc-grps = system
> > tau_t = 0.1
> > ref_t = 298.15
> >
> > ; Pressure coupling is on
> > pcoupl= berendsen
> > pcoupltype= surface-tension
> > tau_p= 2.0  2.0
> > ref_p= 1440  1.0
> > compressibility = 4.46e-5  0
> > refcoord_scaling= com
> >
> > ; Periodic boundary conditions
> > pbc = xyz
> >
> > ; Dispersion correction
> > DispCorr = EnerPres
> >
> > ; Velocity generation
> > gen_vel = yes
> > lincs_warnangle = 90
> >
> >
> > Now I'm gonna using semiisotropic instead of surface tension like in the
> > following:
> > pcoupltyp   = semiisotropic
> > tau_p = 0.5
> > ref_p  = 1.0  1.0
> > compressibility = 4.46e-5  0
> >
> > Thank you for your help.
> > Sincerely,
> > Iman
> >
> > On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
> > imanahmadabad...@gmail.com> wrote:
> >
> >> Dear All Users,
> >>
> >> I'm calculating the surface tension of the water, my box contains almost
> >> 5000 water molecule in the middle of that. Through NVT equilibration, I
> got
> >> reasonable results for surface tension but when I use NPT for my system,
> >> the system crashes every time. The pressure coupling options are in the
> >> following:
> >>
> >> pcoupltyp = surface-tension
> >> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
> >> three values)
> >> ref_p  = 1440  1.0
> >> compressibility = 4.46e-5  0
> >>
> >> first ref-p value is 720*2 = 1440. 720 is the surface tension of water
> in
> >> 298.15.
> >>
> >> Now, I'm going to use semiisotropic for P-coupling:
> >>
> >> pcoupltyp   = semiisotropic
> >> tau_p = 0.5
> >> ref_p  = 1.0  1.0
> >> compressibility = 4.46e-5  0
> >>
> >> Could I have any recommendation about my problem with surface-tension
> >> pcoupltyp? Am I right with semiisotropic options?
> >>
> >>
> >> Respectfully,
> >> Iman Ahmadabadi
> >>
> >
> >
> >
> > --
> > Iman Ahmadabadi
> >
> > Sharif University of Technology, Tehran, Iran
> >
> > Department of Physics and Chemistry
> >
> > Phone: (+98) 9156125273
> >
> > Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
> >
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
> --
> 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] Surface tension for water

[Iman Ahmadabadi]

Hi Dan,

There is no error massage, It's just a crashing and stopping the
simulation. The version is 4.6.0.

Iman

On Tue, Aug 29, 2017 at 9:57 PM, Iman Ahmadabadi  wrote:

> Dear Dan,
>
> I have attached the NPT.mdp file in the following:
>
> title =  NPT equilibration
> ; Run parameters
> integrator = md
> nsteps = 2000
> dt= 0.001
>
> ; Output control
> nstxout = 500
> nstvout = 500
> nstenergy = 500
> nstlog = 500
>
> ; Bond parameters
> continuation= no
> constraint_algorithm= lincs
> constraints= all-bonds
> lincs_iter= 1
> lincs_order= 4
>
> ; Neighborsearching
> cutoff-scheme   = Verlet
> ns_type= grid
> nstlist= 20
> rlist   = 2.0
> rcoulomb= 2.0
> rvdw= 2.0
>
> ; Electrostatics
> coulombtype= PME
> pme_order= 4
> fourierspacing = 0.12
>
> ; Temperature coupling is on
> tcoupl = V-rescale
> tc-grps = system
> tau_t = 0.1
> ref_t = 298.15
>
> ; Pressure coupling is on
> pcoupl= berendsen
> pcoupltype= surface-tension
> tau_p= 2.0  2.0
> ref_p= 1440  1.0
> compressibility = 4.46e-5  0
> refcoord_scaling= com
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Dispersion correction
> DispCorr = EnerPres
>
> ; Velocity generation
> gen_vel = yes
> lincs_warnangle = 90
>
>
> Now I'm gonna using semiisotropic instead of surface tension like in the
> following:
> pcoupltyp   = semiisotropic
> tau_p = 0.5
> ref_p  = 1.0  1.0
> compressibility = 4.46e-5  0
>
> Thank you for your help.
> Sincerely,
> Iman
>
> On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear All Users,
>>
>> I'm calculating the surface tension of the water, my box contains almost
>> 5000 water molecule in the middle of that. Through NVT equilibration, I got
>> reasonable results for surface tension but when I use NPT for my system,
>> the system crashes every time. The pressure coupling options are in the
>> following:
>>
>> pcoupltyp = surface-tension
>> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
>> three values)
>> ref_p  = 1440  1.0
>> compressibility = 4.46e-5  0
>>
>> first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
>> 298.15.
>>
>> Now, I'm going to use semiisotropic for P-coupling:
>>
>> pcoupltyp   = semiisotropic
>> tau_p = 0.5
>> ref_p  = 1.0  1.0
>> compressibility = 4.46e-5  0
>>
>> Could I have any recommendation about my problem with surface-tension
>> pcoupltyp? Am I right with semiisotropic options?
>>
>>
>> Respectfully,
>> Iman Ahmadabadi
>>
>
>
>
> --
> Iman Ahmadabadi
>
> Sharif University of Technology, Tehran, Iran
>
> Department of Physics and Chemistry
>
> Phone: (+98) 9156125273
>
> Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
>



-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Phone: (+98) 9156125273

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
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Re: [gmx-users] Surface Tension Calculation

[Lei]

Hi, Dan,
Thanks  for your response. The interfacial tensions I get from gmx energy
is way larger than the typical surface free energy of solid. So I suspect
the freeze command may have generated some artifacts and I need to find a
better force field.
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Re: [gmx-users] Surface tension for water

[Iman Ahmadabadi]

Dear Dan,

I have attached the NPT.mdp file in the following:

title =  NPT equilibration
; Run parameters
integrator = md
nsteps = 2000
dt= 0.001

; Output control
nstxout = 500
nstvout = 500
nstenergy = 500
nstlog = 500

; Bond parameters
continuation= no
constraint_algorithm= lincs
constraints= all-bonds
lincs_iter= 1
lincs_order= 4

; Neighborsearching
cutoff-scheme   = Verlet
ns_type= grid
nstlist= 20
rlist   = 2.0
rcoulomb= 2.0
rvdw= 2.0

; Electrostatics
coulombtype= PME
pme_order= 4
fourierspacing = 0.12

; Temperature coupling is on
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 298.15

; Pressure coupling is on
pcoupl= berendsen
pcoupltype= surface-tension
tau_p= 2.0  2.0
ref_p= 1440  1.0
compressibility = 4.46e-5  0
refcoord_scaling= com

; Periodic boundary conditions
pbc = xyz

; Dispersion correction
DispCorr = EnerPres

; Velocity generation
gen_vel = yes
lincs_warnangle = 90


Now I'm gonna using semiisotropic instead of surface tension like in the
following:
pcoupltyp   = semiisotropic
tau_p = 0.5
ref_p  = 1.0  1.0
compressibility = 4.46e-5  0

Thank you for your help.
Sincerely,
Iman

On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi  wrote:

> Dear All Users,
>
> I'm calculating the surface tension of the water, my box contains almost
> 5000 water molecule in the middle of that. Through NVT equilibration, I got
> reasonable results for surface tension but when I use NPT for my system,
> the system crashes every time. The pressure coupling options are in the
> following:
>
> pcoupltyp = surface-tension
> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all
> three values)
> ref_p  = 1440  1.0
> compressibility = 4.46e-5  0
>
> first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
> 298.15.
>
> Now, I'm going to use semiisotropic for P-coupling:
>
> pcoupltyp   = semiisotropic
> tau_p = 0.5
> ref_p  = 1.0  1.0
> compressibility = 4.46e-5  0
>
> Could I have any recommendation about my problem with surface-tension
> pcoupltyp? Am I right with semiisotropic options?
>
>
> Respectfully,
> Iman Ahmadabadi
>



-- 
Iman Ahmadabadi

Sharif University of Technology, Tehran, Iran

Department of Physics and Chemistry

Phone: (+98) 9156125273

Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] pullx (gromacs 4.6 vs 2016)

[gromacs query]

Hi All,

Am just wondering if somebody has seen this in different gmx versions?

Thanks.
JIom


On Fri, Aug 25, 2017 at 11:00 AM, gromacs query 
wrote:

> Hi All,
>
> I am using 'equivalent' mdp settings for pull run in Gromacs 4.6 and 2016.
>
> With gromacs 4.6 I get time, 0Z and 1dZ; which I can understand as
> explained here:  https://www.mail-archive.com/g
> mx-us...@gromacs.org/msg22453.html
>
> With Gromacs 2016 I get only time and some distance and xvg file says is
> Position. Is it same as 1dZ? Just wondering why 0Z is not printed.
>
> #> pull settings for 4.6<
>
> pull= umbrella
> pull_geometry   = direction ;
> pull-vec1 = 0 0 -1
> pull_dim= N N Y ;
> pull_start  = yes   ; define initial COM distance > 0
> pull_ngroups= 1
> pull_group0 = Mem ; restrained group
> pull_group1 = Peptide; group to pull
> pull_init1 = 0
> pull_rate1  = 0.0; nm per ps
> pull_k1 = 1000   ; kJ mol^-1 nm^-2
> pull-nstxout = 1000;
> pull-nstfout = 1000;
> ;;
>
>
> #> pull settings for 2016<
>
> pull = yes
> pull_coord1_type= umbrella ; equivalent to  pull = umbrella
> pull_coord1_geometry= direction   ; equivalent to pull_geometry   =
> direction ;
> pull-coord1-vec = 0 0 -1  ; equivalent to pull-vec1 = 0 0 -1
> pull_coord1_dim  = N N Y   ; equivalent to pull_dim = N N Y ;
> pull_coord1_start = yes; equivalent to pull_start  = yes ; define
> initial COM distance > 0
> pull_ngroups= 2   ; equivalent to pull_ngroups= 1
> pull_coord1_groups  = 1 2
> pull_group1_name= Mem   ; equivalent to  pull_group0
> pull_group2_name= Peptide ; equivalent to
> pull_group1
> pull-coord1-init= 0   ;  pull_init1 = 0
> pull_coord1_rate= 0.0   ; equivalent to pull_rate1
> pull_coord1_k   = 1000   ; equivalent to pull_k1 =
> 1000   ; kJ mol^-1 nm^-2
>
>
> Thanks
>
> JIom
>
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Re: [gmx-users] Surface Tension Calculation

[Dan Gil]

Hi Lei,

1. In the Gromacs manual you can find the formula that the software uses to
calculate surface tension. It is just based on a few components of the
pressure tensor, so I imagine you can just use gmx energy (or g_energy
depending on the version of Gromacs you are using).
2. Freezing doesn't sound like a good idea if you are trying to calculate
the surface tension from equilibrium states. Here is a quote from the
online gromacs manual:

> Non-equilibrium MDnon-equilibrium MD*freezegrps:*Groups that are to be
> frozen (i.e. their X, Y, and/or Z position will not be updated; e.g. Lipid
> SOL). *freezedim* specifies for which dimension the freezing applies. To
> avoid spurious contibrutions to the virial and pressure due to large forces
> between completely frozen atoms you need to use energy group exclusions
> , this also saves
> computing time. Note that coordinates of frozen atoms are not scaled by
> pressure-coupling algorithms.


In essence, you have to be very knowledgeable about what you are doing.
First of all, this section is under non-equilibrium MD so it already seems
like a bad idea. Freezing the solid phase seems like a bad idea because it
will affect how the solid lattice responds to pressure changes. If you
really know what you are doing, perhaps you can use energy group exclusions
as the manual suggests. But I think that if you have a good force-field for
the solid phase it should be stable even without freezing. Have you tried
simulating without freeze? After careful equilibration and then a
sufficiently long production run, what result do you get for the
interfacial tension from gmx energy?
3. I don't yet see why anything like position restraints or freeze is
necessary.

Dan

On Mon, Aug 28, 2017 at 4:39 PM, Lei  wrote:

> Hi, gmx users,
> I have some questions regarding the surface tension calculation in gromacs.
> I was running simulations about interface between phase 1 (solid) and phase
> 2 (liquid). In my production run, the phase 1 molecules are frozen and I
> need to calculate the interfacial tension between phase 1 and phase 2.  I
> followed the typical procedure to calculate the surface tension: phase 1 is
> sandwiched by phase 2 and the interface is planar.
> So my questions are:
> 1. Is there a way to calculate the interfacial tension between phase 1 and
> phase 2?
> 2. Does the freeze command affect the calculation of tension? Do I need to
> freeze phase 1 atoms in the simulation to calculate the interfacial tension
> between phase 1 and phase 2?
> 3. What if I applied the position restraints on the phase 1 atoms instead
> of freezing them?
> Thank you all and enjoy simulating.
> --
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Re: [gmx-users] Surface tension for water

[Dan Gil]

What is the error message?
What version of Gromacs are you using?
Can you post the entire .mdp file?


On Tue, Aug 29, 2017 at 9:34 AM, Iman Ahmadabadi  wrote:

> Dear All Users,
>
> I'm calculating the surface tension of the water, my box contains almost
> 5000 water molecule in the middle of that. Through NVT equilibration, I got
> reasonable results for surface tension but when I use NPT for my system,
> the system crashes every time. The pressure coupling options are in the
> following:
>
> pcoupltyp = surface-tension
> tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all three
> values)
> ref_p  = 1440  1.0
> compressibility = 4.46e-5  0
>
> first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
> 298.15.
>
> Now, I'm going to use semiisotropic for P-coupling:
>
> pcoupltyp   = semiisotropic
> tau_p = 0.5
> ref_p  = 1.0  1.0
> compressibility = 4.46e-5  0
>
> Could I have any recommendation about my problem with surface-tension
> pcoupltyp? Am I right with semiisotropic options?
>
>
> Respectfully,
> Iman Ahmadabadi
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[gmx-users] Surface tension for water

[Iman Ahmadabadi]

Dear All Users,

I'm calculating the surface tension of the water, my box contains almost
5000 water molecule in the middle of that. Through NVT equilibration, I got
reasonable results for surface tension but when I use NPT for my system,
the system crashes every time. The pressure coupling options are in the
following:

pcoupltyp = surface-tension
tau_p= 0.5  0.5  &  1.0  1.0  &  2.0  2.0  (Crashing with all three
values)
ref_p  = 1440  1.0
compressibility = 4.46e-5  0

first ref-p value is 720*2 = 1440. 720 is the surface tension of water in
298.15.

Now, I'm going to use semiisotropic for P-coupling:

pcoupltyp   = semiisotropic
tau_p = 0.5
ref_p  = 1.0  1.0
compressibility = 4.46e-5  0

Could I have any recommendation about my problem with surface-tension
pcoupltyp? Am I right with semiisotropic options?


Respectfully,
Iman Ahmadabadi
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Re: [gmx-users] Difference in hydrogen bond lifetimes with and without pbc

[Apramita Chand]

Dear Eric and other Gromacs users,
Thanks for clarifying about how different timescale of trajectories can
affect lifetimes
But the case with and without pbc have same length of trajectories (100 ns).
Then why the difference in lifetimes ( 1793ps with pbc and 2345 without pbc)
Which can be regarded as more accurate?

Yours sincerely,
Apramita
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Re: [gmx-users] gmx analyze Luzar analysis

[Valerio Ferrario]

Thank you!

But still I do not understand what those values represents since there
isn´t a legend in the gmx analyze output. I understood that those 3 values
should be the average hbond lifetime, and the 2 constant k and k´. Am I
correct ?

The fitting is bad since I used long simulation time analysis... Reducing
the time I obtain the same relaxation values With better integrals:

Hydrogen bond thermodynamics at T = 300 K
One-way 0.030 33.376  13.321
Integral   0.085 11.729  10.713
Relaxation  1.038  0.963   4.478

Valerio


2017-08-29 14:01 GMT+02:00 Erik Marklund :

> Dear Valerio,
>
> Have a glance at the paper by Luzar and Chandler.
>
> Btw: your data doesn’t fit with the kinetic model very well, hence the
> -666 for the integral.
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4539
> erik.markl...@kemi.uu.se
>
> On 29 Aug 2017, at 13:52, Valerio Ferrario  mailto:valerio.ferra...@gmail.com>> wrote:
>
> Dear all,
>
> I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds
> with -ac option but resulted in segmentation fault. Therefore from the
> normal gmx hbond output I used gmx analyze to obtain the autocorrelation
> function. Therefore, using again gmx analyze with -luzar options and the
> autorrelated xvg as input I want to calculate the hbonds parameters. I have
> an output like this:
>
> Hydrogen bond thermodynamics at T = 300 K
> One-way 0.006156.395   17.174
> Integral  -0.076- 13.220-666.000
> Relaxation  1.0380.963 4.478
>
> So my question is: what are the different values? I do not understand what
> those values indicate since no "legend" is provide. I guess that 2 of the 3
> values for relaxation might be k and k´ (rate constant for breaking and
> reforming hbonds), but I am not sure... Can anyone help me in interpreting
> those numbers?
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Erik Marklund]

Dear Apramita,

Right. Still, the same still applies with regards to the -666.

It could be a matter of statistics, why you get sensible values for the longer 
trajectory chunk. Also, note that the trajectory length limits the possible 
timescales that the model can tease out. If I understand correctly, your 
trajectories with and without pic have different length, so I’m not surprised 
that the kinetic constants that you get out are different.

Kind regards,
Erik

__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 29 Aug 2017, at 14:02, Apramita Chand 
> wrote:

Dear Eric,
Its actually the DG(kj/mol) value  which is -666. The time is coming to
be-126 ps. But the g_hbond is failing to fit the kinetic model to the data
for the last 60ns as you have implied. Any reasons why this could have
happened, while for the entire trajectory, I am getting positive values?
But for the entire trajectory, with and without pbc(1793ps and 2345ps
respectively) , I have two separate values for lifetime. Which one should I
take?

I would be appreciative of any suggestions

Looking forward to your help,

yours sincerely
Apramita

















*Message:( 2 Date: Tue, 29 Aug 2017 08:09:32 + From: Erik Marklund
 
>> To:
"gmx-us...@gromacs.org 
>" 

>> Subject: Re: [gmx-users] 
Difference in Hydrogen
Bond Lifetimes on truncating trajectory and also on using pbc
Message-ID: 

>>
 Content-Type:
text/plain; charset="utf-8" Dear Apramita, IIRC, the time is set to.-666
when gmx hbond fails to fit the kinetic model to the data. Not the most
informative way of indicating an error perhaps. Kind regards, Erik
__*



* Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow
Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4539
erik.markl...@kemi.uu.se 
><*

*mailto:erik.markl...@kemi.uu.se 
>> On 29 Aug
2017, at 07:20, Apramita Chand 

><*



















*mailto:apramita.ch...@gmail.com 

Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Apramita Chand]

Dear Eric,
Its actually the DG(kj/mol) value  which is -666. The time is coming to
be-126 ps. But the g_hbond is failing to fit the kinetic model to the data
for the last 60ns as you have implied. Any reasons why this could have
happened, while for the entire trajectory, I am getting positive values?
But for the entire trajectory, with and without pbc(1793ps and 2345ps
respectively) , I have two separate values for lifetime. Which one should I
take?

I would be appreciative of any suggestions

Looking forward to your help,

yours sincerely
Apramita

















*Message:( 2 Date: Tue, 29 Aug 2017 08:09:32 + From: Erik Marklund
> To:
"gmx-us...@gromacs.org " > Subject: Re: [gmx-users] Difference in Hydrogen
Bond Lifetimes on truncating trajectory and also on using pbc
Message-ID: > Content-Type:
text/plain; charset="utf-8" Dear Apramita, IIRC, the time is set to.-666
when gmx hbond fails to fit the kinetic model to the data. Not the most
informative way of indicating an error perhaps. Kind regards, Erik
__*



* Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow
Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4539
erik.markl...@kemi.uu.se <*

*mailto:erik.markl...@kemi.uu.se > On 29 Aug
2017, at 07:20, Apramita Chand <*



















*mailto:apramita.ch...@gmail.com >> wrote: Dear
All, I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.
Initially, I thought it would be better to analyse hydrogen bonds in last
60ns of simulation, so I truncated the trajectory using g_trjconv using -b
4 -e 10 as options. The results came as *ACF
10628/10628Normalization for c(t) = 0.0621737 for gh(t) = 2.07246e-06Back
Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen bond
thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q =
  0-*


























*-Type Rate (1/ps) Time (ps)  DG (kJ/mol)
Chi^2Forward-0.008 -126.851-666.000  2.8733* (This came for
both with and without pbc). I also tried to do it from the g_hbond command
itself by giving starting time as 40ns and ending as 100ns, but again it
came negative lifetime. Next, I tried g_trjconv with application of -pbc
mol -ur compact options on untruncated(100ns) trajectory. The results came
as: *ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) =
1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 =3.03095Q =
  0-*




















*-Type Rate (1/ps) Time (ps)  DG (kJ/mol)
Chi^2Forward 0.001 1793.775  23.259 3.03095* When I tried
the same with the original unconverted trajectory(without g_trjconv
,without pbc options), I got a lifetime of *2345.890ps*. *My question is
,1) why do the truncated trajectories give negative values for my
simulation?* *2)If I take the whole 100ns for analysis of hydrogen bond
lifetime, which value should I take, since application of pbc gives a
different value than that of the original trajectory value of lifetime.* I
would be very grateful for your help. Looking forward to your suggestions
Yours sincerely Apramita Chand*
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Re: [gmx-users] gmx analyze Luzar analysis

[Erik Marklund]

Dear Valerio,

Have a glance at the paper by Luzar and Chandler.

Btw: your data doesn’t fit with the kinetic model very well, hence the -666 for 
the integral.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se

On 29 Aug 2017, at 13:52, Valerio Ferrario 
> wrote:

Dear all,

I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds
with -ac option but resulted in segmentation fault. Therefore from the
normal gmx hbond output I used gmx analyze to obtain the autocorrelation
function. Therefore, using again gmx analyze with -luzar options and the
autorrelated xvg as input I want to calculate the hbonds parameters. I have
an output like this:

Hydrogen bond thermodynamics at T = 300 K
One-way 0.006156.395   17.174
Integral  -0.076- 13.220-666.000
Relaxation  1.0380.963 4.478

So my question is: what are the different values? I do not understand what
those values indicate since no "legend" is provide. I guess that 2 of the 3
values for relaxation might be k and k´ (rate constant for breaking and
reforming hbonds), but I am not sure... Can anyone help me in interpreting
those numbers?
--
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[gmx-users] gmx analyze Luzar analysis

[Valerio Ferrario]

Dear all,

I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds
with -ac option but resulted in segmentation fault. Therefore from the
normal gmx hbond output I used gmx analyze to obtain the autocorrelation
function. Therefore, using again gmx analyze with -luzar options and the
autorrelated xvg as input I want to calculate the hbonds parameters. I have
an output like this:

Hydrogen bond thermodynamics at T = 300 K
One-way 0.006156.395   17.174
Integral  -0.076- 13.220-666.000
Relaxation  1.0380.963 4.478

So my question is: what are the different values? I do not understand what
those values indicate since no "legend" is provide. I guess that 2 of the 3
values for relaxation might be k and k´ (rate constant for breaking and
reforming hbonds), but I am not sure... Can anyone help me in interpreting
those numbers?
-- 
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Re: [gmx-users] Unable to install 5.1.14

[Rajat Desikan]

Installing version 2016.3 worked perfectly. Thanks!

Regards,
Rajat

On Mon, Aug 28, 2017 at 12:08 PM, Vytautas Rakeviius  wrote:

> You have updated boost so you have to update GROMACS too. 2016.3 is the
> latest version you should download it.
> Another possibility is to downgrade boost to older, but you can bump into
> other mish-mash issues. I do not recommend that.
>
>
>
> On Sunday, August 27, 2017, 11:36:21 PM GMT+3, Rajat Desikan <
> rajatdesi...@gmail.com> wrote:
>
> Dear All,
> I had removed gromacs 5.1.14. from my system (Ubuntu 16.04) a while ago,
> and I'm having trouble reinstalling it. Cmake runs fine, but the system
> repeatedly fails in the make step with this weird error:
>
> [  3%] Building CXX object src/gromacs/CMakeFiles/
> libgromacs.dir/listed-forces/pairs.cpp.o
> [  3%] Building CXX object src/gromacs/CMakeFiles/
> libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o
> In file included from /usr/local/include/boost/exception/detail/exception_
> ptr.hpp:20:0,
> from /usr/local/include/boost/exception_ptr.hpp:9,
> from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
> utility/exceptions.h:53,
> from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
> commandline/cmdlineprogramcontext.cpp:62:
> /usr/local/include/boost/exception/info.hpp: In member function ‘virtual
> boost::shared_ptr
> boost::exception_detail::error_info_container_impl::get(const
> boost::exception_detail::type_info_&) const’:
> /usr/local/include/boost/exception/info.hpp:102:28: error: use of deleted
> function ‘boost::shared_ptr base>::shared_ptr(const
> boost::shared_ptr&)’
> return p;
> ^
> In file included from /usr/local/include/boost/shared_ptr.hpp:17:0,
> from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
> commandline/cmdlineprogramcontext.h:54,
> from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/
> commandline/cmdlineprogramcontext.cpp:47:
> /usr/local/include/boost/smart_ptr/shared_ptr.hpp:168:25: note:
> ‘boost::shared_ptr base>::shared_ptr(const
> boost::shared_ptr&)’ is
> implicitly declared as deleted because ‘boost::shared_ptr exception_detail::error_info_base>’ declares a move constructor or move
> assignment operator
>
> There are similar errors after this, and make fails. I have updated boost
> on my system (version 58), and my system has the latest upgrades. Can
> anyone please point out the way ahead? I've exhausted all easy options (Eg.
> cleanly remove all gromacs associated files, redownload, untar and try to
> install).
>
> My cmake command is:
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs514 -DGMX_USE_RDTSCP=off
>
> I've tried other permutations of the above command (without
> -DGMX_USE_RDTSCP=off
> for instance) and nothing seems to work.
>
> Thank you for your time.
>
> Regards,
> Rajat
>
> --
> Dr. Rajat Desikan (Post Doctoral Fellow)
> Prof. Narendra M Dixit's Lab (no 1),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
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-- 
Dr. Rajat Desikan (Post Doctoral Fellow)
Prof. Narendra M Dixit's Lab (no 1),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] gromacs error

[Justin Lemkul]

On 8/29/17 12:09 AM, Neha Gupta wrote:

Hi Vytautas,

Thank you for your response..

I did as you told and got this message at the command prompt

libfftw3f: /usr/local/lib/libfftw3f.la /usr/local/lib/libfftw3f.a

But the error tells me :

gmx: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory

Even when I go to that location, namely, /usr/local/lib. I do not find "
libfftw3f.so.3."

What is the next step?


It's hard to even follow what you've done.  If GROMACS couldn't find 
FFTW when installing, even that should have failed.  It appears you've 
compiled FFTW statically whereas GROMACS expected shared objects.  
Revisit how you compiled everything, and perhaps start over so you do 
things consistently.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
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Re: [gmx-users] nstcomm < nstcalenergy

[Justin Lemkul]

On 8/29/17 1:47 AM, Simon Kit Sang Chu wrote:

Dear every user,

I am using Andersen thermostat and nstcomm should be set to 1 (step).
However, after specifying nstcomm = 1, an error has returned -

nstcalenergy cannot be smaller than nstcomm. GROMACS automatically sets it
to nstcalenergy step.


I fail to search for "nstcalenergy" in neither mdp nor manual.


It's there, and has been for several years:

http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#output-control

If you're using an algorithm that requires global summation of energy 
terms, or otherwise limited by algorithmic requirements as you are here, 
you have to sum the energies at every step.  This slows things down, but 
in some cases (like yours) it's required.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] nstcomm < nstcalenergy

[yujie liu]

Hi，
Firstly, you should confirm your gromacs version, gromacs 5.x certainly 
includes nstcalenergy options in .mdp file. So you must set nstcalenergy=1 
while  the default value is 10 in .mdp if you want to nstcomm=1.

thanks
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[gmx-users] Coordination vs cumulative number in gmx_rdf

[Dilip H N]

Hello,
In the command to calculate rdf,
gmx rdf -f md.trr -s md.tpr -n abc.ndx -o rdf_abc.xvg -cn cn_abc.xvg
Is the cumulative number obtained using the -cn flag with gmx_rdf same as
coordination number?
If not, then how can I calculate coordination number from cumulative
number? or how can i calculate the corresponding coordination number in
with gromacs tools ..??

Any suggestions are highly appreciated...

Thank you..
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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