Re: [gmx-users] gmx check precision

2018-03-30 Thread Justin Lemkul 



On 3/30/18 7:29 AM, jt555 wrote:

Hello there,

I am currently using GROMACS version 5.1.2 and had a question in relation to 
the gmx check command. The following appears on the screen after invocation of 
gmx check -f protein.pdb:

GROMACS:  gmx check, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
   gmx check -f protein.pdb

Checking file protein.pdb
Reading frame   0 time0.000
# Atoms  9190
Precision 0.0001 (nm)
'GROtesk MACabre and Sinister t=  40.0', 9190 atoms
Reading frame6000 time 24.000

Item#frames Timestep (ps)
Step  625040
Time  625040
Lambda   0
Coords625040
Velocities   0
Forces   0
Box  0

The precision = 0.001 nm, all my attempts at locating the answer for my 
questions proved futile.
Question) Invocation of similar command for XTC file (i.e., gmx check -f 
protein.xtc) also results in precision of 0.001 nm. However, in the manual it 
clearly states that .xtc exhibits greater precision in comparison to .pdb. If


Where does it say that?


that is the case, then why am I observing the same value for precision in both? 
Or is it the case that because the


The default precision for an .xtc file is exactly what you're seeing, 
unless you're changing it in the .mdp file to save more decimal places.



system under investigation only contains 9,190 atoms, therefore the difference 
in precision between .xtc and .pdb is almost negligible and only realised when 
a much larger system is under investigation? FInally, could you kindly


The precision of output files is not related to the size of the systems.


summarise the significance of precision obtained from gmx check command for a 
beginner?


It's just reporting how many decimal places are saved.

-Justin


I thank you in advance for your kind assistance.

Yours faithfully,

J.

Sent with [ProtonMail](https://protonmail.com) Secure Email.


--
==

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

303 Engel Hall
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Blacksburg, VA 24061

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[gmx-users] gmx check precision

2018-03-30 Thread jt555 
Hello there,

I am currently using GROMACS version 5.1.2 and had a question in relation to 
the gmx check command. The following appears on the screen after invocation of 
gmx check -f protein.pdb:

GROMACS:  gmx check, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx check -f protein.pdb

Checking file protein.pdb
Reading frame   0 time0.000
# Atoms  9190
Precision 0.0001 (nm)
'GROtesk MACabre and Sinister t=  40.0', 9190 atoms
Reading frame6000 time 24.000

Item#frames Timestep (ps)
Step  625040
Time  625040
Lambda   0
Coords625040
Velocities   0
Forces   0
Box  0

The precision = 0.001 nm, all my attempts at locating the answer for my 
questions proved futile.
Question) Invocation of similar command for XTC file (i.e., gmx check -f 
protein.xtc) also results in precision of 0.001 nm. However, in the manual it 
clearly states that .xtc exhibits greater precision in comparison to .pdb. If 
that is the case, then why am I observing the same value for precision in both? 
Or is it the case that because the system under investigation only contains 
9,190 atoms, therefore the difference in precision between .xtc and .pdb is 
almost negligible and only realised when a much larger system is under 
investigation? FInally, could you kindly summarise the significance of 
precision obtained from gmx check command for a beginner?

I thank you in advance for your kind assistance.

Yours faithfully,

J.

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Re: [gmx-users] gmx check

2017-07-28 Thread Dawid das 
Thank you for explaining.

Best wishes,
Dawid

2017-07-28 15:11 GMT+02:00 Mark Abraham :

> Hi,
>
> Seems like the extremes of normal variation of unconstrained bonds. As gmx
> help check suggests, the feature exists as a quick sanity check. The use of
> "correct" is in the sense of "between sensible atom indices" rather than
> suggesting that only one length is valid.
>
> Mark
>
> On Fri, 28 Jul 2017 14:41 Dawid das  wrote:
>
> > Hi,
> >
> > No, those bonds I get the message were not constrained and virtually in
> > every frame there is different
> > bunch of bonds for which I get this message. Because the whole output
> from
> > gmx check is 1.1 GB,
> > I just give you a few examples.
> >
> > Reading frame   0 time0.000
> > # Atoms  24884
> > Precision 0.001 (nm)
> > Distance between atoms 53 and 55 is 0.149, should be 0.143
> > Distance between atoms 55 and 66 is 0.159, should be 0.149
> > Distance between atoms 70 and 81 is 0.155, should be 0.149
> > Distance between atoms 72 and 75 is 0.160, should be 0.153
> > Distance between atoms 102 and 104 is 0.152, should be 0.143
> > Distance between atoms 104 and 120 is 0.154, should be 0.149
> > .
> > .
> > .
> >
> > then
> >
> > Reading frame   1 time2.000   Distance between atoms 11 and 13 is
> > 0.139, should be 0.134
> > Distance between atoms 15 and 17 is 0.162, should be 0.154
> > Distance between atoms 26 and 28 is 0.148, should be 0.154
> > Distance between atoms 26 and 44 is 0.158, should be 0.149
> > Distance between atoms 31 and 34 is 0.147, should be 0.153
> > Distance between atoms 48 and 51 is 0.155, should be 0.149
> > Distance between atoms 51 and 53 is 0.129, should be 0.134
> > Distance between atoms 55 and 57 is 0.160, should be 0.154
> > Distance between atoms 55 and 66 is 0.154, should be 0.149
> > Distance between atoms 70 and 81 is 0.159, should be 0.149
> > Distance between atoms 78 and 79 is 0.121, should be 0.126
> > Distance between atoms 81 and 82 is 0.119, should be 0.123
> > .
> > .
> > .
> > and so on. What do you think about that?
> >
> > Best wishes,
> > Dawid
> >
> > 2017-07-28 13:33 GMT+02:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > It's hard to tell without seeing the messages and knowing whether those
> > > bonds were constrained.
> > >
> > > Mark
> > >
> > > On Fri, 28 Jul 2017 13:19 Dawid das  wrote:
> > >
> > > > Dear Gromacs Users,
> > > >
> > > > I get a bunch of communicates when I run
> > > > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
> > > >
> > > > saying that I get different bond lengths than they should be. Can
> that
> > be
> > > > caused by only 0.001 nm precision of my results?
> > > > Also I am not exactly sure if I understand correctly what I am
> checking
> > > > here.
> > > > "If both a trajectory and a .tpr <
> > > > http://manual.gromacs.org/online/tpr.html>
> > > > file are given (with -s1) the program will check whether the bond
> > lengths
> > > > defined in the tpr  file
> > are
> > > > indeed correct in the trajectory."
> > > > If so, then what does it mean "correct" in this sentence? It is
> pretty
> > > > obvious that
> > > > bond lengths vary during simulation unless I constrain them.
> > > >
> > > > Best wishes,
> > > > Dawid Grabarek
> > > > --
> > > > Gromacs Users mailing list
> > > >
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> > > > posting!
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Re: [gmx-users] gmx check

2017-07-28 Thread Mark Abraham 
Hi,

Seems like the extremes of normal variation of unconstrained bonds. As gmx
help check suggests, the feature exists as a quick sanity check. The use of
"correct" is in the sense of "between sensible atom indices" rather than
suggesting that only one length is valid.

Mark

On Fri, 28 Jul 2017 14:41 Dawid das  wrote:

> Hi,
>
> No, those bonds I get the message were not constrained and virtually in
> every frame there is different
> bunch of bonds for which I get this message. Because the whole output from
> gmx check is 1.1 GB,
> I just give you a few examples.
>
> Reading frame   0 time0.000
> # Atoms  24884
> Precision 0.001 (nm)
> Distance between atoms 53 and 55 is 0.149, should be 0.143
> Distance between atoms 55 and 66 is 0.159, should be 0.149
> Distance between atoms 70 and 81 is 0.155, should be 0.149
> Distance between atoms 72 and 75 is 0.160, should be 0.153
> Distance between atoms 102 and 104 is 0.152, should be 0.143
> Distance between atoms 104 and 120 is 0.154, should be 0.149
> .
> .
> .
>
> then
>
> Reading frame   1 time2.000   Distance between atoms 11 and 13 is
> 0.139, should be 0.134
> Distance between atoms 15 and 17 is 0.162, should be 0.154
> Distance between atoms 26 and 28 is 0.148, should be 0.154
> Distance between atoms 26 and 44 is 0.158, should be 0.149
> Distance between atoms 31 and 34 is 0.147, should be 0.153
> Distance between atoms 48 and 51 is 0.155, should be 0.149
> Distance between atoms 51 and 53 is 0.129, should be 0.134
> Distance between atoms 55 and 57 is 0.160, should be 0.154
> Distance between atoms 55 and 66 is 0.154, should be 0.149
> Distance between atoms 70 and 81 is 0.159, should be 0.149
> Distance between atoms 78 and 79 is 0.121, should be 0.126
> Distance between atoms 81 and 82 is 0.119, should be 0.123
> .
> .
> .
> and so on. What do you think about that?
>
> Best wishes,
> Dawid
>
> 2017-07-28 13:33 GMT+02:00 Mark Abraham :
>
> > Hi,
> >
> > It's hard to tell without seeing the messages and knowing whether those
> > bonds were constrained.
> >
> > Mark
> >
> > On Fri, 28 Jul 2017 13:19 Dawid das  wrote:
> >
> > > Dear Gromacs Users,
> > >
> > > I get a bunch of communicates when I run
> > > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
> > >
> > > saying that I get different bond lengths than they should be. Can that
> be
> > > caused by only 0.001 nm precision of my results?
> > > Also I am not exactly sure if I understand correctly what I am checking
> > > here.
> > > "If both a trajectory and a .tpr <
> > > http://manual.gromacs.org/online/tpr.html>
> > > file are given (with -s1) the program will check whether the bond
> lengths
> > > defined in the tpr  file
> are
> > > indeed correct in the trajectory."
> > > If so, then what does it mean "correct" in this sentence? It is pretty
> > > obvious that
> > > bond lengths vary during simulation unless I constrain them.
> > >
> > > Best wishes,
> > > Dawid Grabarek
> > > --
> > > 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] gmx check

2017-07-28 Thread Dawid das 
Hi,

No, those bonds I get the message were not constrained and virtually in
every frame there is different
bunch of bonds for which I get this message. Because the whole output from
gmx check is 1.1 GB,
I just give you a few examples.

Reading frame   0 time0.000
# Atoms  24884
Precision 0.001 (nm)
Distance between atoms 53 and 55 is 0.149, should be 0.143
Distance between atoms 55 and 66 is 0.159, should be 0.149
Distance between atoms 70 and 81 is 0.155, should be 0.149
Distance between atoms 72 and 75 is 0.160, should be 0.153
Distance between atoms 102 and 104 is 0.152, should be 0.143
Distance between atoms 104 and 120 is 0.154, should be 0.149
.
.
.

then

Reading frame   1 time2.000   Distance between atoms 11 and 13 is
0.139, should be 0.134
Distance between atoms 15 and 17 is 0.162, should be 0.154
Distance between atoms 26 and 28 is 0.148, should be 0.154
Distance between atoms 26 and 44 is 0.158, should be 0.149
Distance between atoms 31 and 34 is 0.147, should be 0.153
Distance between atoms 48 and 51 is 0.155, should be 0.149
Distance between atoms 51 and 53 is 0.129, should be 0.134
Distance between atoms 55 and 57 is 0.160, should be 0.154
Distance between atoms 55 and 66 is 0.154, should be 0.149
Distance between atoms 70 and 81 is 0.159, should be 0.149
Distance between atoms 78 and 79 is 0.121, should be 0.126
Distance between atoms 81 and 82 is 0.119, should be 0.123
.
.
.
and so on. What do you think about that?

Best wishes,
Dawid

2017-07-28 13:33 GMT+02:00 Mark Abraham :

> Hi,
>
> It's hard to tell without seeing the messages and knowing whether those
> bonds were constrained.
>
> Mark
>
> On Fri, 28 Jul 2017 13:19 Dawid das  wrote:
>
> > Dear Gromacs Users,
> >
> > I get a bunch of communicates when I run
> > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
> >
> > saying that I get different bond lengths than they should be. Can that be
> > caused by only 0.001 nm precision of my results?
> > Also I am not exactly sure if I understand correctly what I am checking
> > here.
> > "If both a trajectory and a .tpr <
> > http://manual.gromacs.org/online/tpr.html>
> > file are given (with -s1) the program will check whether the bond lengths
> > defined in the tpr  file are
> > indeed correct in the trajectory."
> > If so, then what does it mean "correct" in this sentence? It is pretty
> > obvious that
> > bond lengths vary during simulation unless I constrain them.
> >
> > Best wishes,
> > Dawid Grabarek
> > --
> > 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] gmx check

2017-07-28 Thread Mark Abraham 
Hi,

It's hard to tell without seeing the messages and knowing whether those
bonds were constrained.

Mark

On Fri, 28 Jul 2017 13:19 Dawid das  wrote:

> Dear Gromacs Users,
>
> I get a bunch of communicates when I run
> gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
>
> saying that I get different bond lengths than they should be. Can that be
> caused by only 0.001 nm precision of my results?
> Also I am not exactly sure if I understand correctly what I am checking
> here.
> "If both a trajectory and a .tpr <
> http://manual.gromacs.org/online/tpr.html>
> file are given (with -s1) the program will check whether the bond lengths
> defined in the tpr  file are
> indeed correct in the trajectory."
> If so, then what does it mean "correct" in this sentence? It is pretty
> obvious that
> bond lengths vary during simulation unless I constrain them.
>
> Best wishes,
> Dawid Grabarek
> --
> 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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>
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[gmx-users] gmx check

2017-07-28 Thread Dawid das 
Dear Gromacs Users,

I get a bunch of communicates when I run
gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out

saying that I get different bond lengths than they should be. Can that be
caused by only 0.001 nm precision of my results?
Also I am not exactly sure if I understand correctly what I am checking
here.
"If both a trajectory and a .tpr 
file are given (with -s1) the program will check whether the bond lengths
defined in the tpr  file are
indeed correct in the trajectory."
If so, then what does it mean "correct" in this sentence? It is pretty
obvious that
bond lengths vary during simulation unless I constrain them.

Best wishes,
Dawid Grabarek
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