subject:"\[gmx\-users\] need help \!"

Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

2020-05-08 Thread Ekatherina O


Hello  Justin Lemkul,
Thank you for the suggestions. I understood and already tried using 
transforms with trjconv. The picture got better.



--

Message: 4
Date: Thu, 7 May 2020 08:17:06 -0400
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Message-ID: 
Content-Type: text/plain; charset=utf-8; format=flowed



On 5/7/20 4:24 AM, Ekatherina O wrote:

Hello Dr. Dallas Warren,
Thank you for the suggestions.

But this does not solve the problem of the movement of atoms of quartz
layers (upper and lower) located at the borders of the box. I would
like the quartz layers to remain intact during the modeling process,
i.e. atoms did not move and the initial structure was disturbed. How
can I solve this problem?


I will reiterate what Dallas has said - if you have atoms that are
exactly at the bottom of the box, they effectively *are* the boundary
and therefore can seem to "jump" back and forth. This has no 
implication

whatsoever on the physics, just visualization. You can "fix" the issue
after the fact with trjconv.


Can I freeze structure (atoms)? Since with a further increase in
simulation time, I observe the movement of quartz layers in the box. I
don?t need them to move.



Freezing is very artificial and leads to unphysical collisions. Avoid 
if

at all possible.



--
Yours sincerely,
Ekatherina O.
o...@isc-ras.ru
--
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Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

2020-05-08 Thread Ekatherina O


Hello Debashish,

Thank you for the suggestions.
Could you tell us in more detail how (in which file) postion restraints 
on them in x, y, z should be written by putting force constant of [1000 
1000 1000

Could you please advise the links where I can read about it?


Message: 3
Date: Thu, 7 May 2020 14:14:41 +0200
From: Debashish Banerjee 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Hello Ekatherina, I did not reach a point in my simulations where I 
have
used freeze command, but I think for your case, can't you put a 
position
constraint on your quartz layer. In that case, you just have to create 
an

index file having quartz in the group and then you can put postion
restraints on them in x,y,z by putting force constant of [1000 1000 
1000]

so that the layer doesn't move.

Regards,
Debashish

--
Yours sincerely,
Ekatherina O.
o...@isc-ras.ru
--
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Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

2020-05-07 Thread Debashish Banerjee

Hello Justin, so I believe it's just pbc visualization stuff going on
then.. okay.. yes you can do it then from trjconv .

Regards,
Debashish

On Thu, 7 May 2020, 14:14 Debashish Banerjee, 
wrote:

> Hello Ekatherina, I did not reach a point in my simulations where I have
> used freeze command, but I think for your case, can't you put a position
> constraint on your quartz layer. In that case, you just have to create an
> index file having quartz in the group and then you can put postion
> restraints on them in x,y,z by putting force constant of [1000 1000 1000]
> so that the layer doesn't move.
>
> Regards,
> Debashish
>
>
>
>
>
> On Thu, 7 May 2020, 10:28 Ekatherina O,  wrote:
>
>> Hello Dr. Dallas Warren,
>> Thank you for the suggestions.
>>
>> But this does not solve the problem of the movement of atoms of quartz
>> layers (upper and lower) located at the borders of the box. I would like
>> the quartz layers to remain intact during the modeling process, i.e.
>> atoms did not move and the initial structure was disturbed. How can I
>> solve this problem?
>> Can I freeze structure (atoms)? Since with a further increase in
>> simulation time, I observe the movement of quartz layers in the box. I
>> don’t need them to move.
>>
>> > Message: 4
>> > Date: Tue, 5 May 2020 09:12:51 +1000
>> > From: Dallas Warren 
>> > To: GROMACS users 
>> > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
>> > Message-ID:
>> >   > dtxkx86ohdbsdyjg2ma2+tpa8ge...@mail.gmail.com>
>> > Content-Type: text/plain; charset="UTF-8"
>> >
>> > 1/ it means that between the original coordinate file loaded with vmd
>> > and
>> > the frame you are looking at there from the trajectory file, those
>> > atoms
>> > have moved across the periodic boundary and vmd is still drawing the
>> > bond
>> > between them. vmd knows nothing about bonds, it guesses where the bonds
>> > should be and maintains them between those atoms when viewing a
>> > trajectory.
>> > If looking to make a nice looking animation simply using gmx trjconv to
>> > move the layer into the center of the box. Otherwise use a viewing
>> > method
>> > in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws
>> > each frame i.e. DynamicBonds
>> >
>> > 2/ where the simulation box is located is entirely arbitrary. So if it
>> > is
>> > not in the location you want then use gmx trjconv to move it to where
>> > you
>> > want it to be.
>> >
>> > All these things you are seeing here are artifacts of the periodic
>> > boundary
>> > condition:
>> >
>> http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc
>> >
>> >
>> > Catch ya,
>> >
>> > Dr. Dallas Warren
>> > Drug Delivery, Disposition and Dynamics
>> > Monash Institute of Pharmaceutical Sciences, Monash University
>> > 381 Royal Parade, Parkville VIC 3052
>> > dallas.war...@monash.edu
>> > -
>> > When the only tool you own is a hammer, every problem begins to
>> > resemble a
>> > nail.
>>
>> --
>> Yours sincerely,
>> Ekatherina O.
>> o...@isc-ras.ru
>> --
>> 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] Need help creating md.mdp for silica(quartz)?

2020-05-07 Thread Justin Lemkul




On 5/7/20 4:24 AM, Ekatherina O wrote:

Hello Dr. Dallas Warren,
Thank you for the suggestions.

But this does not solve the problem of the movement of atoms of quartz 
layers (upper and lower) located at the borders of the box. I would 
like the quartz layers to remain intact during the modeling process, 
i.e. atoms did not move and the initial structure was disturbed. How 
can I solve this problem?


I will reiterate what Dallas has said - if you have atoms that are 
exactly at the bottom of the box, they effectively *are* the boundary 
and therefore can seem to "jump" back and forth. This has no implication 
whatsoever on the physics, just visualization. You can "fix" the issue 
after the fact with trjconv.


Can I freeze structure (atoms)? Since with a further increase in 
simulation time, I observe the movement of quartz layers in the box. I 
don’t need them to move.




Freezing is very artificial and leads to unphysical collisions. Avoid if 
at all possible.


-Justin


Message: 4
Date: Tue, 5 May 2020 09:12:51 +1000
From: Dallas Warren 
To: GROMACS users 
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Message-ID:

Content-Type: text/plain; charset="UTF-8"

1/ it means that between the original coordinate file loaded with vmd 
and

the frame you are looking at there from the trajectory file, those atoms
have moved across the periodic boundary and vmd is still drawing the 
bond

between them. vmd knows nothing about bonds, it guesses where the bonds
should be and maintains them between those atoms when viewing a 
trajectory.

If looking to make a nice looking animation simply using gmx trjconv to
move the layer into the center of the box. Otherwise use a viewing 
method

in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws
each frame i.e. DynamicBonds

2/ where the simulation box is located is entirely arbitrary. So if 
it is
not in the location you want then use gmx trjconv to move it to where 
you

want it to be.

All these things you are seeing here are artifacts of the periodic 
boundary

condition:
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc 




Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to 
resemble a

nail.




--
==

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

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Need help creating md.mdp for silica(quartz)?

2020-05-07 Thread Debashish Banerjee

Hello Ekatherina, I did not reach a point in my simulations where I have
used freeze command, but I think for your case, can't you put a position
constraint on your quartz layer. In that case, you just have to create an
index file having quartz in the group and then you can put postion
restraints on them in x,y,z by putting force constant of [1000 1000 1000]
so that the layer doesn't move.

Regards,
Debashish





On Thu, 7 May 2020, 10:28 Ekatherina O,  wrote:

> Hello Dr. Dallas Warren,
> Thank you for the suggestions.
>
> But this does not solve the problem of the movement of atoms of quartz
> layers (upper and lower) located at the borders of the box. I would like
> the quartz layers to remain intact during the modeling process, i.e.
> atoms did not move and the initial structure was disturbed. How can I
> solve this problem?
> Can I freeze structure (atoms)? Since with a further increase in
> simulation time, I observe the movement of quartz layers in the box. I
> don’t need them to move.
>
> > Message: 4
> > Date: Tue, 5 May 2020 09:12:51 +1000
> > From: Dallas Warren 
> > To: GROMACS users 
> > Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
> > Message-ID:
> >dtxkx86ohdbsdyjg2ma2+tpa8ge...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > 1/ it means that between the original coordinate file loaded with vmd
> > and
> > the frame you are looking at there from the trajectory file, those
> > atoms
> > have moved across the periodic boundary and vmd is still drawing the
> > bond
> > between them. vmd knows nothing about bonds, it guesses where the bonds
> > should be and maintains them between those atoms when viewing a
> > trajectory.
> > If looking to make a nice looking animation simply using gmx trjconv to
> > move the layer into the center of the box. Otherwise use a viewing
> > method
> > in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws
> > each frame i.e. DynamicBonds
> >
> > 2/ where the simulation box is located is entirely arbitrary. So if it
> > is
> > not in the location you want then use gmx trjconv to move it to where
> > you
> > want it to be.
> >
> > All these things you are seeing here are artifacts of the periodic
> > boundary
> > condition:
> >
> http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc
> >
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.war...@monash.edu
> > -
> > When the only tool you own is a hammer, every problem begins to
> > resemble a
> > nail.
>
> --
> Yours sincerely,
> Ekatherina O.
> o...@isc-ras.ru
> --
> 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] Need help creating md.mdp for silica(quartz)?

2020-05-07 Thread Ekatherina O


Hello Dr. Dallas Warren,
Thank you for the suggestions.

But this does not solve the problem of the movement of atoms of quartz 
layers (upper and lower) located at the borders of the box. I would like 
the quartz layers to remain intact during the modeling process, i.e. 
atoms did not move and the initial structure was disturbed. How can I 
solve this problem?
Can I freeze structure (atoms)? Since with a further increase in 
simulation time, I observe the movement of quartz layers in the box. I 
don’t need them to move.



Message: 4
Date: Tue, 5 May 2020 09:12:51 +1000
From: Dallas Warren 
To: GROMACS users 
Subject: Re: [gmx-users] Need help creating md.mdp for silica(quartz)?
Message-ID:

Content-Type: text/plain; charset="UTF-8"

1/ it means that between the original coordinate file loaded with vmd 
and
the frame you are looking at there from the trajectory file, those 
atoms
have moved across the periodic boundary and vmd is still drawing the 
bond

between them. vmd knows nothing about bonds, it guesses where the bonds
should be and maintains them between those atoms when viewing a 
trajectory.

If looking to make a nice looking animation simply using gmx trjconv to
move the layer into the center of the box. Otherwise use a viewing 
method

in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws
each frame i.e. DynamicBonds

2/ where the simulation box is located is entirely arbitrary. So if it 
is
not in the location you want then use gmx trjconv to move it to where 
you

want it to be.

All these things you are seeing here are artifacts of the periodic 
boundary

condition:
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to 
resemble a

nail.


--
Yours sincerely,
Ekatherina O.
o...@isc-ras.ru
--
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] Need help creating md.mdp for silica(quartz)?

2020-05-04 Thread Dallas Warren

1/ it means that between the original coordinate file loaded with vmd and
the frame you are looking at there from the trajectory file, those atoms
have moved across the periodic boundary and vmd is still drawing the bond
between them. vmd knows nothing about bonds, it guesses where the bonds
should be and maintains them between those atoms when viewing a trajectory.
If looking to make a nice looking animation simply using gmx trjconv to
move the layer into the center of the box. Otherwise use a viewing method
in vmd that doesn't draw the bonds i.e. VDW, Points or one that redraws
each frame i.e. DynamicBonds

2/ where the simulation box is located is entirely arbitrary. So if it is
not in the location you want then use gmx trjconv to move it to where you
want it to be.

All these things you are seeing here are artifacts of the periodic boundary
condition:
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#gmx-pbc

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.

On Mon, 4 May 2020 at 22:08, Ekatherina O  wrote:

> I have done simulation water in nanopore based on quartz (I use model
> ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is
> a link to the pictures at the initial time (1.png) and in the modeling
> process.
>
> https://drive.google.com/drive/folders/1GpIyx8___kQ3Zbe36wkSSINxgtKwIWsn?usp=sharing
> )
> Its NVT simulation (see .mdp below) and neutral charge on surface (have
> silanol groups), system is overall neutral.
> 1) Did I choose the right settings?  What do these atomic displacements
> (lines in the pictures) mean? What restrictions should be imposed on the
> system?
> 2) In addition, I noticed that all the atoms of the quartz walls that
> are in the vicinity of the box walls move from the upper wall to the
> lower and lower to the upper. How can I avoid this when periodic
> boundary conditions are imposed? Do I understand correctly that this
> involves interaction between the quartz walls?
>
> integrator  =  md-vv
> dt  =  0.001; = 1 fs
> nsteps  =  50   ; = 100  ps
> nstcomm =  1
> ; OUTPUT CONTROL OPTIONS
> nstxout =  200
> nstvout =  200
> nstfout =  200
> nstlog  =  200
> nstenergy   =  200
> energygrps  =  System
> cutoff-scheme= Verlet
> ; NEIGHBORSEARCHING PARAMETERS
> ;periodic-molecules  =  no
> nstlist =  20
> ns_type =  grid
> pbc =  xyz
> rlist   =  1.4
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype =  PME  ; fourierspacing ; pme-order
> ;   =  PPPM ; fourierspacing
> ;   =  Ewald; No parallel Ewald.
> rcoulomb=  1.4
> rvdw=  1.4
> ; Ewald, PME, PPPM options
> ;fourierspacing  =  0.12
> ;fourier_nx  =  0   ; 2 3 5 7
> ;fourier_ny =   0
> ;fourier_nz =   0
> ;pme_order  =  6; 10 ; 8 ; default = 4
> optimize_fft=  yes
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> Tcoupl  =  nose-hoover
> tc-grps =  System
> tau_t   =  0.5
> ref_t   =  298
> ;Pcoupl  =  berendsen
> pcoupltype  =  isotropic
> tau_p   =  0.1
> compressibility = 0.0008076
> ref_p   = 800
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel =  yes
> gen_temp=  298
> gen_seed=  173529
> ; OPTIONS FOR BONDS
> constraints =  all-bonds
> constraint-algorithm = lincs
>
>
> And sorry if I missed similar topic in mailing list, but I couldn't find
> anything similar.
>
>
> --
> Yours sincerely,
> Ekatherina O.
> o...@isc-ras.ru
> --
> 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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[gmx-users] Need help creating md.mdp for silica(quartz)?

2020-05-04 Thread Ekatherina O

I have done simulation water in nanopore based on quartz (I use model 
ClayFF) using Gromacs 5.1.5 and have observed strange behavior. (Here is 
a link to the pictures at the initial time (1.png) and in the modeling 
process.

https://drive.google.com/drive/folders/1GpIyx8___kQ3Zbe36wkSSINxgtKwIWsn?usp=sharing)
Its NVT simulation (see .mdp below) and neutral charge on surface (have 
silanol groups), system is overall neutral.
1) Did I choose the right settings?  What do these atomic displacements 
(lines in the pictures) mean? What restrictions should be imposed on the 
system?
2) In addition, I noticed that all the atoms of the quartz walls that 
are in the vicinity of the box walls move from the upper wall to the 
lower and lower to the upper. How can I avoid this when periodic 
boundary conditions are imposed? Do I understand correctly that this 
involves interaction between the quartz walls?


integrator  =  md-vv
dt  =  0.001; = 1 fs
nsteps  =  50   ; = 100  ps
nstcomm =  1
; OUTPUT CONTROL OPTIONS
nstxout =  200
nstvout =  200
nstfout =  200
nstlog  =  200
nstenergy   =  200
energygrps  =  System
cutoff-scheme= Verlet
; NEIGHBORSEARCHING PARAMETERS
;periodic-molecules  =  no
nstlist =  20
ns_type =  grid
pbc =  xyz
rlist   =  1.4
; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype =  PME  ; fourierspacing ; pme-order
;   =  PPPM ; fourierspacing
;   =  Ewald; No parallel Ewald.
rcoulomb=  1.4
rvdw=  1.4
; Ewald, PME, PPPM options
;fourierspacing  =  0.12
;fourier_nx  =  0   ; 2 3 5 7
;fourier_ny =   0
;fourier_nz =   0
;pme_order  =  6; 10 ; 8 ; default = 4
optimize_fft=  yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
Tcoupl  =  nose-hoover
tc-grps =  System
tau_t   =  0.5
ref_t   =  298
;Pcoupl  =  berendsen
pcoupltype  =  isotropic
tau_p   =  0.1
compressibility = 0.0008076
ref_p   = 800
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel =  yes
gen_temp=  298
gen_seed=  173529
; OPTIONS FOR BONDS
constraints =  all-bonds
constraint-algorithm = lincs


And sorry if I missed similar topic in mailing list, but I couldn't find 
anything similar.



--
Yours sincerely,
Ekatherina O.
o...@isc-ras.ru
--
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Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2020-01-10 Thread Schulz, Roland

Hi,

It needs to be on its own line prior to the void.
What will be in next version of GROMACS (2019.6 and 2020.1) is:
https://gerrit.gromacs.org/c/gromacs/+/15218/4/src/gromacs/pulling/pullutil.cpp

You don't need the #ifdef/#endif if you only care about compiling with ICC.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>  On Behalf Of
> Cardenas, Alfredo E
> Sent: Friday, January 10, 2020 12:00 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Need help with installation of Gromacs-2019.3 with
> Intell compilers
> 
> Hi Roland and others gmx-users,
> I am also getting a similar compilation error regarding pullutil.cpp:
> 
> icpc: error #10106: Fatal error in
> /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by floating point exception compilation aborted for
> /home1/01247/alfredo/Software/gromacs-
> 2019.4/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
> 
> using optimization for AVX512. I saw this post where you suggested a work-
> around adding "#pragma intel optimization_level 2" in front of
> pull_calc_coms. I see the line in pullutil.cpp:
> 
> void pull_calc_coms(const t_commrec *cr,
> pull_t *pull,
> const t_mdatoms *md,
> t_pbc *pbc,
> double t,
> const rvec x[], rvec *xp) {
> 
> I tried putting the pragma before void and it gave me a bunch of errors.
> Where exactly should it be added?
> Thanks,
> 
> Alfredo
> --
> 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.
-- 
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
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mail to gmx-users-requ...@gromacs.org.

[gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2020-01-10 Thread Cardenas, Alfredo E

Hi Roland and others gmx-users,
I am also getting a similar compilation error regarding pullutil.cpp:

icpc: error #10106: Fatal error in 
/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom, 
terminated by floating point exception
compilation aborted for 
/home1/01247/alfredo/Software/gromacs-2019.4/src/gromacs/pulling/pullutil.cpp 
(code 1)
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o] 
Error 1
make[2]: *** Waiting for unfinished jobs
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

using optimization for AVX512. I saw this post where you suggested a 
work-around adding "#pragma intel optimization_level 2" in front of 
pull_calc_coms. I see the line in pullutil.cpp:

void pull_calc_coms(const t_commrec *cr,
pull_t *pull,
const t_mdatoms *md,
t_pbc *pbc,
double t,
const rvec x[], rvec *xp)
{

I tried putting the pragma before void and it gave me a bunch of errors. Where 
exactly should it be added?
Thanks,

Alfredo
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2020-01-06 Thread Schulz, Roland

Hi,

As a work-around it is possible to put "#pragma intel optimization_level 2" in 
front pull_calc_coms in file src/gromacs/pulling/pullutil.cpp or use Intel 
compiler 2019u4 which doesn't have the problem.
Lowering the optimization for the one function shouldn't have a significant 
impact on performance even if you use pulling because this function isn't 
compute intensive. A full fix is in the works.

Roland

> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
>  On Behalf Of Rajib
> Biswas
> Sent: Monday, December 30, 2019 6:13 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Need help with installation of Gromacs-2019.3 with
> Intell compilers
> 
> Dear Gromacs-Users,
> 
> Is there any update on this issue? I have used the following flags for version
> 2019.3
> 
> /apps/codes/cmake/3.15.4/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -
> DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
> -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -
> DCMAKE_C_COMPILER=mpiicc -DCMAKE_CXX_COMPILER=mpiicpc -
> DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_BUILD_MDRUN_ONLY=ON
> 
> and getting compilation error which says:
> 
> [ 58%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
> icpc: error #10105:
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(-497903120)
> icpc: error #10106: Fatal error in
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
> 
> Your help will be highly appreciated.
> 
> Thanking you.
> 
> With regards,
> Rajib
> 
> 
> 
> On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh 
> wrote:
> 
> > I have tried this command line:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -
> DGMX_OPENMP=ON
> > -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
> > -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON
> > which had no errors for *cmake* or *make -j 4*, but *make check* gave
> > me an
> > error:
> > ...
> > [100%] Running all tests except physical validation Test project
> > /home/doroshl/gromacs-2019.3/build
> >   Start  1: TestUtilsUnitTests
> >  1/46 Test  #1: TestUtilsUnitTests ..***Failed0.00 sec
> > /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while
> > loading shared libraries: libmkl_intel_lp64.so: cannot open shared
> > object file: No such file or directory ...
> > 0% tests passed, 46 tests failed out of 46
> >
> > so I included libmkl_intel_lp64.so:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir
> >
> > -
> DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019
> .5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
> > -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
> > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64 -
> L/usr/bin/gcc/lib64"
> > -DGMX_MPI=ON -DGMX_OPENMP=ON -
> DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
> > -DGMX_SIMD=SSE2 -
> DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out which doesn't give
> any error
> > messages for cmake, but then in *sudo make -j
> > 4 *results in
> >
> > [ 46%] Building CXX object
> > src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o
> > icpc: error #10105:
> >
> >
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/int
> el64/mcpcom:
> > core dumped
> > icpc: warning #10102: unknown signal(694380720)
> > icpc: error #10106: Fatal error in
> >
> > /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/
> > intel64/mcpcom,
> > terminated by unknown
> > compilation aborted for
> > /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> > src/gromacs/CMakeFiles/libgromacs.

Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2020-01-01 Thread Lyudmyla Dorosh

Dear Rajib,

Originally I have made too many irreversible changes to my ubuntu trying to
fit requirements, including nvidia cuda and openMPI. Hence segmentation
fault and system started crushing in general. Since then I re-installed
Ununtu, Intel drivers and libraries, newest version of cmake.

Ubuntu 18.04.3 LTS
Intel® Parallel Studio XE 2019
gromacs-2018.8.tar.gz
 fftw-3.3.8.tar.gz
cmake-3.16.0-rc1-Linux-x86_64.tar.gz

Sourced Intel compilers:
source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/impi/2019.5.281/intel64/bin/mpivars.sh
source /opt/intel/mkl/bin/mklvars.sh intel64

Runned cmake install using the flags:
sudo cmake .. -DBUILD_SHARED_LIBS=off -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=on -DGMX_OPENMP=on
-DGMX_CYCLE_SUBCOUNTERS=on -DGMX_GPU=off -DGMX_SIMD=SSE2
-DCMAKE_C_COMPILER="/opt/intel/bin/icc"
-DCMAKE_CXX_COMPILER="/opt/intel/bin/icpc" -DREGRESSIONTEST_DOWNLOAD=on

Now it works perfectly, performance just great.
Fantastic reply from Quin K - THANKS.
Hope it helps,
Lyudmyla


On Mon, Dec 30, 2019 at 7:15 AM Rajib Biswas  wrote:

> Dear Gromacs-Users,
>
> Is there any update on this issue? I have used the following flags for
> version 2019.3
>
> /apps/codes/cmake/3.15.4/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
>  -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc
> -DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON
> -DGMX_BUILD_MDRUN_ONLY=ON
>
> and getting compilation error which says:
>
> [ 58%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
> icpc: error #10105:
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(-497903120)
> icpc: error #10106: Fatal error in
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> Your help will be highly appreciated.
>
> Thanking you.
>
> With regards,
> Rajib
>
>
>
> On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh  wrote:
>
> > I have tried this command line:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON
> > -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
> > -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON
> > which had no errors for *cmake* or *make -j 4*, but *make check* gave me
> an
> > error:
> > ...
> > [100%] Running all tests except physical validation
> > Test project /home/doroshl/gromacs-2019.3/build
> >   Start  1: TestUtilsUnitTests
> >  1/46 Test  #1: TestUtilsUnitTests ..***Failed0.00
> sec
> > /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while
> loading
> > shared libraries: libmkl_intel_lp64.so: cannot open shared object file:
> No
> > such file or directory
> > ...
> > 0% tests passed, 46 tests failed out of 46
> >
> > so I included libmkl_intel_lp64.so:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir
> >
> >
> -DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
> > -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
> > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64
> -L/usr/bin/gcc/lib64"
> > -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
> > -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out
> > which doesn't give any error messages for cmake, but then in *sudo make
> -j
> > 4 *results in
> >
> > [ 46%] Building CXX object
> > src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o
> > icpc: error #10105:
> >
> >
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> > core dumped
> > icpc: warning #10102: unknown signal(694380720)
> > icpc: error #10106: Fatal error in
> >
> >
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> > terminated by unknown
> > compilation aborted for
> > /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> > src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for target
> > 'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o' failed
> > make[2]: ***
> [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> > Error 1
>

Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2019-12-30 Thread Quin K

Here are some details I gathered over some time and how I overcame the
issue of *slow running gromacs* due to not using all threads in the intel
processor.

* Install according to following videos*
https://www.youtube.com/watch?v=vOJsmtFeSGk

https://www.youtube.com/watch?v=BZNzYt_DUB0


SIMD value different for various processors.

If this value is not given during gromacs dirty installation the run will
be very slow.


Problem of slow running gromacs
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-October/092874.html


-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_USE_RDTSCP=ON
-DGMX_SIMD=AVX2_256

Add above line when doing command during dirty installation of gromacs

cmake *gromacs_extraction_folder_location* -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256



Windows installation after enabling Linux subsystem

 cmake /mnt/d/gmx/gromacs-2018.7/  -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_USE_RDTSCP=ON -DGMX_SIMD=AVX2_256


http://manual.gromacs.org/documentation/2018/install-guide/index.html

With

tar xfz gromacs-2018.tar.gz

cd gromacs-2018

mkdir build

cd build

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_USE_RDTSCP=ON
-DGMX_SIMD=AVX2_256

make

make check

sudo make install

source /usr/local/gromacs/bin/GMXRC

Email Thread on profiles...@gmaill.com

https://mail.google.com/mail/u/0/#sent/QgrcJHsbfmGnwcmrVLLsVwCnxXgGcqBRJLg

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-June/114030.html

To remove gromacs
https://www.thelinuxfaq.com/ubuntu/ubuntu-17-04-zesty-zapus/gromacs?type=uninstall

Gromacs dirty installation

http://manual.gromacs.org/documentation/2018/install-guide/index.html





On Mon, Dec 30, 2019 at 7:45 PM Rajib Biswas  wrote:

> Dear Gromacs-Users,
>
> Is there any update on this issue? I have used the following flags for
> version 2019.3
>
> /apps/codes/cmake/3.15.4/bin/cmake ..
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
> -DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
>  -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc
> -DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON
> -DGMX_BUILD_MDRUN_ONLY=ON
>
> and getting compilation error which says:
>
> [ 58%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
> icpc: error #10105:
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(-497903120)
> icpc: error #10106: Fatal error in
> /apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> make: *** [all] Error 2
>
> Your help will be highly appreciated.
>
> Thanking you.
>
> With regards,
> Rajib
>
>
>
> On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh  wrote:
>
> > I have tried this command line:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON
> > -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
> > -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON
> > which had no errors for *cmake* or *make -j 4*, but *make check* gave me
> an
> > error:
> > ...
> > [100%] Running all tests except physical validation
> > Test project /home/doroshl/gromacs-2019.3/build
> >   Start  1: TestUtilsUnitTests
> >  1/46 Test  #1: TestUtilsUnitTests ..***Failed0.00
> sec
> > /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while
> loading
> > shared libraries: libmkl_intel_lp64.so: cannot open shared object file:
> No
> > such file or directory
> > ...
> > 0% tests passed, 46 tests failed out of 46
> >
> > so I included libmkl_intel_lp64.so:
> > sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> > -DCMAKE_INSTALL_PREFIX=$installDir
> >
> >
> -DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
> > -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
> > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64
> -L/usr/bin/gcc/lib64"
> > -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
> > -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> > -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> > -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out
> > which doesn't give any error messages for cmake, but then in *sudo make
> -j
> > 4 *results in
> >
> > [ 46%] Building CXX object
> >

Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2019-12-30 Thread Rajib Biswas

Dear Gromacs-Users,

Is there any update on this issue? I have used the following flags for
version 2019.3

/apps/codes/cmake/3.15.4/bin/cmake ..
-DCMAKE_INSTALL_PREFIX=/opt/gromacs/2019.3 -DGMX_FFT_LIBRARY=fftw3
-DCMAKE_PREFIX_PATH=/apps/libs/fftw/3.3.8 -DBUILD_SHARED_LIBS=OFF
 -DGMX_DOUBLE=ON -DGMX_SIMD=AVX2_256 -DCMAKE_C_COMPILER=mpiicc
-DCMAKE_CXX_COMPILER=mpiicpc -DGMX_MPI=ON -DGMX_OPENMP=ON
-DGMX_BUILD_MDRUN_ONLY=ON

and getting compilation error which says:

[ 58%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o
icpc: error #10105:
/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
core dumped
icpc: warning #10102: unknown signal(-497903120)
icpc: error #10106: Fatal error in
/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
terminated by unknown
compilation aborted for
/storage/rajib/opt/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
Error 1
make[2]: *** Waiting for unfinished jobs
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2

Your help will be highly appreciated.

Thanking you.

With regards,
Rajib



On Wed, Oct 9, 2019 at 4:03 AM Lyudmyla Dorosh  wrote:

> I have tried this command line:
> sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> -DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON
> -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
> -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> -DREGRESSIONTEST_DOWNLOAD=ON
> which had no errors for *cmake* or *make -j 4*, but *make check* gave me an
> error:
> ...
> [100%] Running all tests except physical validation
> Test project /home/doroshl/gromacs-2019.3/build
>   Start  1: TestUtilsUnitTests
>  1/46 Test  #1: TestUtilsUnitTests ..***Failed0.00 sec
> /home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while loading
> shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No
> such file or directory
> ...
> 0% tests passed, 46 tests failed out of 46
>
> so I included libmkl_intel_lp64.so:
> sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
> -DCMAKE_INSTALL_PREFIX=$installDir
>
> -DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
> -DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
> -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64 -L/usr/bin/gcc/lib64"
> -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
> -DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
> -DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
> -DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out
> which doesn't give any error messages for cmake, but then in *sudo make -j
> 4 *results in
>
> [ 46%] Building CXX object
> src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o
> icpc: error #10105:
>
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
> core dumped
> icpc: warning #10102: unknown signal(694380720)
> icpc: error #10106: Fatal error in
>
> /home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
> terminated by unknown
> compilation aborted for
> /home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
> src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o' failed
> make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
> Error 1
> make[2]: *** Waiting for unfinished jobs
> CMakeFiles/Makefile2:2499: recipe for target
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:162: recipe for target 'all' failed
> make: *** [all] Error 2
> Thanks for any help
>
>
> On Tue, Oct 8, 2019 at 2:21 AM Paul bauer  wrote:
>
> > Hej,
> >
> > I can't access the repository, so I can't say for certain what happened.
> > Can you share your cmake command line?
> >
> > Cheers
> >
> > Paul
> >
> > On 07/10/2019 21:25, Lyudmyla Dorosh wrote:
> > > Hello Gromacs Developers/Users,
> > >
> > > I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
> > > compilers (+MKL+MPI).
> > > First I compiled cmake with Intel compilers. All output files are
> > attached.
> > > cmake, make seemed to go ok, but all check test failed. What do I do
> > wrong?
> > >
> >
> https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing
> > >
> > > Thank you,
> > >
> > > Lyudmyla Dorosh, PhD
> > > 
> > > University of Alberta
> > > Department of Electrical and Computer Engineering,
> > > 4-021 ECERF
> > > Edmonton, AB, T6G 2G8
> > > Canada
> > > Email: dor...@ualberta.ca

Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2019-10-08 Thread Lyudmyla Dorosh

I have tried this command line:
sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=$installDir -DGMX_MPI=ON -DGMX_OPENMP=ON
-DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF -DGMX_SIMD=SSE2
-DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
-DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
-DREGRESSIONTEST_DOWNLOAD=ON
which had no errors for *cmake* or *make -j 4*, but *make check* gave me an
error:
...
[100%] Running all tests except physical validation
Test project /home/doroshl/gromacs-2019.3/build
  Start  1: TestUtilsUnitTests
 1/46 Test  #1: TestUtilsUnitTests ..***Failed0.00 sec
/home/doroshl/gromacs-2019.3/build/bin/testutils-test: error while loading
shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No
such file or directory
...
0% tests passed, 46 tests failed out of 46

so I included libmkl_intel_lp64.so:
sudo cmake .. -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl
-DCMAKE_INSTALL_PREFIX=$installDir
-DMKL_LIBRARIES="/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so"
-DMKL_INCLUDE_DIR="/home/doroshl/apps/intel/intelpython2/lib"
-DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/bin/gcc/lib64 -L/usr/bin/gcc/lib64"
-DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF
-DGMX_SIMD=SSE2 -DCMAKE_C_COMPILER="/home/doroshl/apps/intel/bin/icc"
-DCMAKE_CXX_COMPILER="/home/doroshl/apps/intel/bin/icpc"
-DREGRESSIONTEST_DOWNLOAD=ON &> cmake.out
which doesn't give any error messages for cmake, but then in *sudo make -j
4 *results in

[ 46%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o
icpc: error #10105:
/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom:
core dumped
icpc: warning #10102: unknown signal(694380720)
icpc: error #10106: Fatal error in
/home/doroshl/apps/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64/mcpcom,
terminated by unknown
compilation aborted for
/home/doroshl/gromacs-2019.3/src/gromacs/pulling/pullutil.cpp (code 1)
src/gromacs/CMakeFiles/libgromacs.dir/build.make:2136: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o' failed
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o]
Error 1
make[2]: *** Waiting for unfinished jobs
CMakeFiles/Makefile2:2499: recipe for target
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2
Thanks for any help


On Tue, Oct 8, 2019 at 2:21 AM Paul bauer  wrote:

> Hej,
>
> I can't access the repository, so I can't say for certain what happened.
> Can you share your cmake command line?
>
> Cheers
>
> Paul
>
> On 07/10/2019 21:25, Lyudmyla Dorosh wrote:
> > Hello Gromacs Developers/Users,
> >
> > I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
> > compilers (+MKL+MPI).
> > First I compiled cmake with Intel compilers. All output files are
> attached.
> > cmake, make seemed to go ok, but all check test failed. What do I do
> wrong?
> >
> https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing
> >
> > Thank you,
> >
> > Lyudmyla Dorosh, PhD
> > 
> > University of Alberta
> > Department of Electrical and Computer Engineering,
> > 4-021 ECERF
> > Edmonton, AB, T6G 2G8
> > Canada
> > Email: dor...@ualberta.ca
> >
>
> --
> Paul Bauer, PhD
> GROMACS Release Manager
> KTH Stockholm, SciLifeLab
> 0046737308594
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


-- 
Regards,

Lyudmyla Dorosh, PhD

University of Alberta
Department of Electrical and Computer Engineering,
4-021 ECERF
Edmonton, AB, T6G 2G8
Canada
Email: dor...@ualberta.ca
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Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2019-10-08 Thread Paul bauer


Hej,

I can't access the repository, so I can't say for certain what happened.
Can you share your cmake command line?

Cheers

Paul

On 07/10/2019 21:25, Lyudmyla Dorosh wrote:

Hello Gromacs Developers/Users,

I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
compilers (+MKL+MPI).
First I compiled cmake with Intel compilers. All output files are attached.
cmake, make seemed to go ok, but all check test failed. What do I do wrong?
https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing

Thank you,

Lyudmyla Dorosh, PhD

University of Alberta
Department of Electrical and Computer Engineering,
4-021 ECERF
Edmonton, AB, T6G 2G8
Canada
Email: dor...@ualberta.ca



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

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[gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

2019-10-07 Thread Lyudmyla Dorosh

Hello Gromacs Developers/Users,

I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
compilers (+MKL+MPI).
First I compiled cmake with Intel compilers. All output files are attached.
cmake, make seemed to go ok, but all check test failed. What do I do wrong?
https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing

Thank you,

Lyudmyla Dorosh, PhD

University of Alberta
Department of Electrical and Computer Engineering,
4-021 ECERF
Edmonton, AB, T6G 2G8
Canada
Email: dor...@ualberta.ca
-- 
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* Please search the archive at 
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Re: [gmx-users] Need help on NVT equilibration for MD simulation of Protein-RNA complex

2017-09-08 Thread Justin Lemkul




On 9/8/17 7:10 AM, Saravanan Parameswaran wrote:


Dear Simulators,,

I am new to MD simulations. I am still learning Gromacs from tutorials and
documentation.

I want to run MD simulation of protein (1700 amino acids) with ssRNA
(around 80 nucleotides) and another dsRNA/dsDNA (around 20-40 nucleotides).

I am trying to understand how protein of interest interacts with
dsDNA/dsRNA/ssDNA/ssRNA. what will be the difference in interactions when
it interacts with different dsDNA/dsRNA/ssDNA/ssRNA and mutational studies
on both protein and dsDNA/dsRNA/ssDNA/ssRNA.

And I am stuck with parameters in ‘initial phase’ NVT equilibration using
Langevin bath which I have found from literature.

I am struggling to find the exact parameters for the protein-DNA/RNA system
to run the three steps of the initial phase: (a) 10ps with increasing
temperature from 0 to 100 K keeping protein & RNA fixed, (b) 25ps with
temperature was further increased upto 200 K keeping backbone atoms of
protein & RNA fixed and (c) 25ps to reach 298 K. Then NPT equilibration for
100 ps at 298 K

After this initial phase, NPT equilibration for 40-50ns followed by
production run in microseconds.

I am not sure how to set parameters for MDP files for the three steps of
the initial phase and NPT equilibration . I have googled it for few days,
but not of much help. I end up with mdp files for free energy analysis only.


Why the NVT equilbration or initial phase is done with three steps in
Langevin bath?


There are many ways to prepare simulation systems.  Some people believe 
in slow warming of a system, others don't.



Why long runs for NPT equilibration?


You have to obtain a stable thermodynamic ensemble; I don't know why 
those authors chose such a time frame (tip: ask them, that's what 
corresponding author contact information is for) but there had to be a 
reason.



Is it really necessary to do production run in microseconds?


Depends on the questions being asked in the simulation.  You have to 
simulate on a time scale sufficient to answer whatever biological 
questions are of interest.




I request you all to provide me the ‘mdp’ files for NVT and NPT
equilibration as well as MD production to run the molecular
dynamics simulations of protein/RNA complex.


If you want to replicate exactly what the authors did, you need to apply 
what is called "simulated annealing."  It is described in the manual 
along with an example.  Custom position restraint files are generated 
with gmx genrestr.  You will need different treatment of restraints in 
each phase described above.


-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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[gmx-users] Need help on NVT equilibration for MD simulation of Protein-RNA complex

2017-09-08 Thread Saravanan Parameswaran


Dear Simulators,,

I am new to MD simulations. I am still learning Gromacs from tutorials and
documentation.

I want to run MD simulation of protein (1700 amino acids) with ssRNA
(around 80 nucleotides) and another dsRNA/dsDNA (around 20-40 nucleotides).

I am trying to understand how protein of interest interacts with
dsDNA/dsRNA/ssDNA/ssRNA. what will be the difference in interactions when
it interacts with different dsDNA/dsRNA/ssDNA/ssRNA and mutational studies
on both protein and dsDNA/dsRNA/ssDNA/ssRNA.

And I am stuck with parameters in ‘initial phase’ NVT equilibration using
Langevin bath which I have found from literature.

I am struggling to find the exact parameters for the protein-DNA/RNA system
to run the three steps of the initial phase: (a) 10ps with increasing
temperature from 0 to 100 K keeping protein & RNA fixed, (b) 25ps with
temperature was further increased upto 200 K keeping backbone atoms of
protein & RNA fixed and (c) 25ps to reach 298 K. Then NPT equilibration for
100 ps at 298 K

After this initial phase, NPT equilibration for 40-50ns followed by
production run in microseconds.

I am not sure how to set parameters for MDP files for the three steps of
the initial phase and NPT equilibration . I have googled it for few days,
but not of much help. I end up with mdp files for free energy analysis only.


Why the NVT equilbration or initial phase is done with three steps in
Langevin bath?

Why long runs for NPT equilibration?

Is it really necessary to do production run in microseconds?


I request you all to provide me the ‘mdp’ files for NVT and NPT
equilibration as well as MD production to run the molecular
dynamics simulations of protein/RNA complex.

I would be really thankful for your kind help.


With Warm Regards,

Saravanan Parameswaran

PostDoctoral Fellow

Gyeongsang National University,

South Korea
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Re: [gmx-users] need help !

2017-03-10 Thread electronsource

Hi

Thanks you for your help .The analyses of my MD work perfectly. 

- Mail original -
De: "Mark Abraham" <mark.j.abra...@gmail.com>
À: gmx-us...@gromacs.org
Envoyé: Jeudi 9 Mars 2017 17:07:07
Objet: Re: [gmx-users] need help !

Hi,

See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Mark

On Thu, Mar 9, 2017 at 5:04 PM <electronsou...@free.fr> wrote:

> Thank you for yours answers .
>
> I'm a felling more comfortable.So to sum up my index file is filled with
> the coordonate that i care.
> So in my case if i want only the RNA i just have to delete all the others
> data.And when i run my .xtc for make it shorter il 'll have only water
> Or i have just to choose the RNA in the menu after using trjconv
>
>
>
> - Mail original -
> De: "Mark Abraham" <mark.j.abra...@gmail.com>
> À: gmx-us...@gromacs.org, "gromacs org gmx-users" <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Envoyé: Jeudi 9 Mars 2017 16:30:36
> Objet: Re: [gmx-users] need help !
>
> Hi,
>
> On Thu, Mar 9, 2017 at 3:11 PM <electronsou...@free.fr> wrote:
>
> > Hello.
> >
> > I am new on using gromacs and i have problems with my files .I need to
> > remove water and ions from an .xtc in order to keep my RNA.Then i have to
> > center the system in the box and remove some frame to be able to
> visualize
> > it.
> >
> > Here are the commands lines that i use:
> >
> > trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx
> >
> > i chose only RNA
> >
> > trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n
> > index.ndx
> >
> > then i convert it into pdb and i remove some frame
> >
> > trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb
> >
> >
> > I have a few question :
> >
> > is my code right ?
> >
>
> Seems plausible.
>
> what do we use index files ?
> >
>
> To specify the indices of subsets of atoms that are of interest.
>
>
> > How can i be sure that i have a good .tpr file because sometimes i have
> > errors.
> >
>
> If it ran your simulation, it's good.
>
> Mark
>
>
> > Tahnks you !!
> >
> >
> >
> > --
> > 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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>
> * 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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Re: [gmx-users] need help !

2017-03-09 Thread Mark Abraham

Hi,

See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume

Mark

On Thu, Mar 9, 2017 at 5:04 PM <electronsou...@free.fr> wrote:

> Thank you for yours answers .
>
> I'm a felling more comfortable.So to sum up my index file is filled with
> the coordonate that i care.
> So in my case if i want only the RNA i just have to delete all the others
> data.And when i run my .xtc for make it shorter il 'll have only water
> Or i have just to choose the RNA in the menu after using trjconv
>
>
>
> - Mail original -
> De: "Mark Abraham" <mark.j.abra...@gmail.com>
> À: gmx-us...@gromacs.org, "gromacs org gmx-users" <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Envoyé: Jeudi 9 Mars 2017 16:30:36
> Objet: Re: [gmx-users] need help !
>
> Hi,
>
> On Thu, Mar 9, 2017 at 3:11 PM <electronsou...@free.fr> wrote:
>
> > Hello.
> >
> > I am new on using gromacs and i have problems with my files .I need to
> > remove water and ions from an .xtc in order to keep my RNA.Then i have to
> > center the system in the box and remove some frame to be able to
> visualize
> > it.
> >
> > Here are the commands lines that i use:
> >
> > trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx
> >
> > i chose only RNA
> >
> > trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n
> > index.ndx
> >
> > then i convert it into pdb and i remove some frame
> >
> > trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb
> >
> >
> > I have a few question :
> >
> > is my code right ?
> >
>
> Seems plausible.
>
> what do we use index files ?
> >
>
> To specify the indices of subsets of atoms that are of interest.
>
>
> > How can i be sure that i have a good .tpr file because sometimes i have
> > errors.
> >
>
> If it ran your simulation, it's good.
>
> Mark
>
>
> > Tahnks you !!
> >
> >
> >
> > --
> > 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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Re: [gmx-users] need help !

2017-03-09 Thread electronsource

Thank you for yours answers .

I'm a felling more comfortable.So to sum up my index file is filled with the 
coordonate that i care.
So in my case if i want only the RNA i just have to delete all the others 
data.And when i run my .xtc for make it shorter il 'll have only water 
Or i have just to choose the RNA in the menu after using trjconv 

- Mail original -
De: "Mark Abraham" <mark.j.abra...@gmail.com>
À: gmx-us...@gromacs.org, "gromacs org gmx-users" 
<gromacs.org_gmx-users@maillist.sys.kth.se>
Envoyé: Jeudi 9 Mars 2017 16:30:36
Objet: Re: [gmx-users] need help !

Hi,

On Thu, Mar 9, 2017 at 3:11 PM <electronsou...@free.fr> wrote:

> Hello.
>
> I am new on using gromacs and i have problems with my files .I need to
> remove water and ions from an .xtc in order to keep my RNA.Then i have to
> center the system in the box and remove some frame to be able to visualize
> it.
>
> Here are the commands lines that i use:
>
> trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx
>
> i chose only RNA
>
> trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n
> index.ndx
>
> then i convert it into pdb and i remove some frame
>
> trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb
>
>
> I have a few question :
>
> is my code right ?
>

Seems plausible.

what do we use index files ?
>

To specify the indices of subsets of atoms that are of interest.

> How can i be sure that i have a good .tpr file because sometimes i have
> errors.
>

If it ran your simulation, it's good.

Mark

> Tahnks you !!
>
>
>
> --
> 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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Re: [gmx-users] need help !

2017-03-09 Thread Mark Abraham

Hi,

On Thu, Mar 9, 2017 at 3:11 PM  wrote:

> Hello.
>
> I am new on using gromacs and i have problems with my files .I need to
> remove water and ions from an .xtc in order to keep my RNA.Then i have to
> center the system in the box and remove some frame to be able to visualize
> it.
>
> Here are the commands lines that i use:
>
> trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx
>
> i chose only RNA
>
> trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n
> index.ndx
>
> then i convert it into pdb and i remove some frame
>
> trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb
>
>
> I have a few question :
>
> is my code right ?
>

Seems plausible.

what do we use index files ?
>

To specify the indices of subsets of atoms that are of interest.


> How can i be sure that i have a good .tpr file because sometimes i have
> errors.
>

If it ran your simulation, it's good.

Mark


> Tahnks you !!
>
>
>
> --
> 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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[gmx-users] need help !

2017-03-09 Thread electronsource

Hello.

I am new on using gromacs and i have problems with my files .I need to remove 
water and ions from an .xtc in order to keep my RNA.Then i have to center the 
system in the box and remove some frame to be able to visualize it.

Here are the commands lines that i use:

trjconv -f gold.xtc -s gold.tpr -o gold_nowater.xtc -n index.ndx

i chose only RNA
 
trjconv -f gold_nowater.xtc -s gold.tpr -o finale_gold.xtc -center -n index.ndx

then i convert it into pdb and i remove some frame 

trjconv -s gold.gro -f gold.xtc -e 2500.0 -o movie.pdb 


I have a few question :

is my code right ?

what do we use index files ?

How can i be sure that i have a good .tpr file because sometimes i have errors.

Tahnks you !!



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[gmx-users] Need Help in Running Thermodynamic Integration (TI) Simulations

2014-07-21 Thread Yew Mun Yip

Hi, I recently tried running TI simulations with a ligand solvated in water
using the CHARMM force field.

When I was running equilibration, everything was fine and the thermodynamic
properties (density, volume, pressure, etc) stabilized.

Then I started my TI simulations.

When I ran till init-lambda = 2, the following error message occurred.

step XXX: Water molecule starting at atom  can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates.

Although visualizing the PDBs generated with VMD does show that the water
molecule have very large bond lengths between the atoms, I'm more concerned
with what could be the problem with my .mdp file that may have lead to this
error?

This is my TI's .mdp file:

; we'll use the sd integrator with 10 time steps (200ps)
integrator   = sd
nsteps   = 10
dt   = 0.002
nstenergy= 1000
nstlog   = 5000
; turn off trajectory writing
nstxout  = 0
nstvout  = 0
; We use the old group scheme because as of writing, the Verlet scheme
; does not support free energy calculations with coupled molecules.
cutoff-scheme= group
; cut-offs at 1.0nm
rlist= 1.0
dispcorr = EnerPres
vdw-type = cut-off
rvdw = 1.0
; Coulomb interactions
coulombtype  = pme
rcoulomb = 1.0
fourierspacing   = 0.12
; Constraints
constraints  = all-bonds
; set temperature to 300K
tcoupl   = v-rescale
tc-grps  = system
tau-t= 0.2
ref-t= 300
; set pressure to 1 bar with a thermostat that gives a correct
; thermodynamic ensemble
pcoupl   = parrinello-rahman
ref-p= 1
compressibility  = 4.5e-5
tau-p= 5
; and set the free energy parameters
free-energy  = yes
couple-moltype   = LIG
; these 'soft-core' parameters make sure we never get overlapping
; charges as lambda goes to 0
sc-power = 1
sc-sigma = 0.3
sc-alpha = 1.0
; we still want the molecule to interact with itself at lambda=0
couple-intramol  = no
couple-lambda1   = vdwq
couple-lambda0   = none
init-lambda-state= 2
; These are the lambda states at which we simulate
; for separate LJ and Coulomb decoupling, use
fep-lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
coul-lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80
0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
vdw-lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00

Any advice is greatly appreciated. =)

-- 
*Yip Yew Mun (Mr)* | PhD Research Scholar | Division of Chemistry
 Biological Chemistry
School of Physical  Mathematical Sciences | Nanyang
Technological University | Singapore 639798
Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sg | GMT+8h
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[gmx-users] Need help for the free energy calculation.

2013-12-30 Thread Rui Zhang

Dear all,
I am doing the free energy calculation using Gromacs 4.6.4 now. However, I
got the message by g_bar:
---
Program g_bar, VERSION 4.6.4
Source code file: /home/rui/Downloads/gromacs-4.6.4/src/tools/gmx_bar.c,
line: 1208

Fatal error:
Could not find a set for foreign lambda = 0.00
in the files for lambda = 0.00
-

Could anyone help me to resolve this problem. Please also see my mdp input:
---

; Run control
integrator   = sd

; Parameters describing what to do, when to stop and what to save
nsteps= 500; Maximum number of (minimization) steps to
perform 12000ns
dt  = 0.002 ; 2fs

; Output control
cutoff-scheme= group
nstlog   = 100
nstenergy= 10
nstcalcenergy = 10
; Neighborsearching and short-range nonbonded interactions
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.2

; Electrostatics
coulombtype  = PME
rcoulomb = 1.2

; van der Waals
vdw-type = cut-off
;rvdw-switch  = 0.9
rvdw = 1.2
;vdw-modifier=Potential-shift-Verlet

; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12

; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no

;Temperature coupling
tcoupl=V-rescale   ;berendsen
tc_grps=Protein CA2+_Water_and_ions
tau_t=0.1 0.1;ps time constant for coupling for each group
ref_t=300 300;K reference temperature

; Pressure coupling
pcoupl = Parrinello-Rahman
Pcoupltype=isotropic
tau_p=0.5
ref_p=1.0
compressibility=4.5e-5
refcoord_scaling=com

; Free energy control stuff
free_energy  = yes
init_lambda  = 0.1
init-lambda-state = -1
delta_lambda = 0
fep-lambdas  = 0 0.2
;coul-laambdas
couple-intramol  = yes
sc-alpha = 0.5
sc-power = 1.0
sc-sigma = 0.3
nstdhdl  = 10

; Generate velocities to start
gen_vel  = no

; Type of constraint algorithm
constraints  = h-bonds
constraint-algorithm = lincs
continuation = yes
ld_seed =-1
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12

; Output control
nstxout  = 1000   ; frequency to write coordinates to
output trajectory file
;energygrps=  Protein;  Which energy group(s) to write to disk

Thank you very much for any help!
Sincerely,

Rui Zhang


-- 

Dr. Rui Zhang
Postdoctoral Research Associate
Department of Veterinary Pathobiology
Texas AM University
College Station, TX 77840
rzhan...@tamu.edu
(305) 301-7879
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Re: [gmx-users] need help !

[gmx-users] need help !

[gmx-users] Need Help in Running Thermodynamic Integration (TI) Simulations

[gmx-users] Need help for the free energy calculation.

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