[gmx-users] electric field

[Maryam Kowsar]

Dear users,

I applied electric fields of different magnitudes (less than 1 v/nm since
higher amounts are avoided) in my system. I have some charged water
molecules and I expected to see very different results when the magnitude
is changed, but haven't got that much difference. How can I be sure that
electric fields worked?
I found the following link that it changed the code of electric field
according to the shape of the system:
 http://www.gromacs.org/Developer_Zone/Programming_Guide/Patching_mdrun
Can the current implemented code in gromacs be applied for all systems or
should I change it for different systems?

Thanks!
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Re: [gmx-users] Problems with trjconv

[Mark Abraham]

Hi,

Certainly. You do not want to convert non-trivial trajectories to text
format.

Mark

On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña  wrote:

> well, I check and it is the same line of command. The biggest file has
> more weight than the .traj file and it is only a .gro file . Is this
> posible?
> Mishelle
> > From: mark.j.abra...@gmail.com
> > Date: Sun, 15 Nov 2015 19:15:50 +
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Problems with trjconv
> >
> > Hi,
> >
> > Either you didn't issue the same command (inspect your terminal history),
> > or the second operation didn't complete (for any number of reasons).
> >
> > Mark
> >
> > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña 
> wrote:
> >
> > > Hello, I have a question about trjconv. I have a .trr file and I put
> the
> > > following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646
> -o
> > > 1646ps.gro I got back a file of 13813272703 bytes. Then I make the
> same and
> > > got a file of 506444 bytes. Do you know what is happening?Mishelle
> > > --
> > > 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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[gmx-users] Problems with trjconv

[Mishelle Oña]

Hello, I have a question about trjconv. I have a .trr file and I put the 
following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 
1646ps.gro I got back a file of 13813272703 bytes. Then I make the same and got 
a file of 506444 bytes. Do you know what is happening?Mishelle  
   
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Re: [gmx-users] Problems with trjconv

[Mishelle Oña]

Eh, I don´t understand what you mean, please  explain me .Mishelle:)

> From: mark.j.abra...@gmail.com
> Date: Sun, 15 Nov 2015 19:28:47 +
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problems with trjconv
> 
> Hi,
> 
> Certainly. You do not want to convert non-trivial trajectories to text
> format.
> 
> Mark
> 
> On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña  wrote:
> 
> > well, I check and it is the same line of command. The biggest file has
> > more weight than the .traj file and it is only a .gro file . Is this
> > posible?
> > Mishelle
> > > From: mark.j.abra...@gmail.com
> > > Date: Sun, 15 Nov 2015 19:15:50 +
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] Problems with trjconv
> > >
> > > Hi,
> > >
> > > Either you didn't issue the same command (inspect your terminal history),
> > > or the second operation didn't complete (for any number of reasons).
> > >
> > > Mark
> > >
> > > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña 
> > wrote:
> > >
> > > > Hello, I have a question about trjconv. I have a .trr file and I put
> > the
> > > > following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646
> > -o
> > > > 1646ps.gro I got back a file of 13813272703 bytes. Then I make the
> > same and
> > > > got a file of 506444 bytes. Do you know what is happening?Mishelle
> > > > --
> > > > 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] restart issues with Gromacs

[Mark Abraham]

Hi,

GROMACS assumes the file systems actually write to disk when you use the
system call that means that, and works correctly if so. But if the file
system or its configuration don't actually do that (for "performance" or
erroneous reasons), then all bets are off. mdrun can't even know if it's
being lied to, because, well, it's being lied to...

Mark

On Sun, 15 Nov 2015 22:30 Nash, Anthony  wrote:

> Hi all,
>
> Running Grimaces 5.0.4 with PLUMED 2.2 on a cluster, number of ranks (MPI
> processes) is 24. The simulation successfully ran for the maximum cluster
> wall time (48 hours).
>
> I attempt to restart the simulations using the following command (with a
> sun microsystem grid engine submission script):
>
> gerun mdrun_mpi_d -deffnm neu_mut_meta_K -cpi neu_mut_meta_K.cpt -noappend
> -plumed
>
>
> However, whilst the queue is telling me that the job is running, the
> *.part0002.log file seems stuck at:
>
> ---
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 1 Y 1
> The minimum size for domain decomposition cells is 1.025 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.43 Y 0.56
> The maximum allowed distance for charge groups involved in interactions is:
>  non-bonded interactions   1.025 nm
> two-body bonded interactions  (-rdd)   1.025 nm
>   multi-body bonded interactions  (-rdd)   1.025 nm
>   atoms separated by up to 5 constraints  (-rcon)  1.025 nm
> 
>
>
> The cluster error file and output file (not gromacs file) contains no
> warnings or errors. The gromacs log file contains no warnings or errors.
>
> I have seen this behaviour quite a number of times, going back to early
> versions of gromacs 4 around late 2010 (I think). I got into the habit of
> a) copying backing up the .cpt files, and b) always using -noappend option
> to preserve the .trr file. Has there ever been an explanation as to why
> this is happening?
>
> Many thanks
> Anthony
>
> --
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Re: [gmx-users] Problems with trjconv

[Mishelle Oña]

Ok, but this erase the frame from my trajectory? because i don´t want to modify 
it.

> Date: Mon, 16 Nov 2015 00:10:07 +0100
> From: shantanu...@gmail.com
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problems with trjconv
> 
> If you want to take out only one frame then you can use -dump option.
> 
> trjconv -f trajcentrada.trr -dump 1646 -o 1646ps.gro
> 
> On Sun, Nov 15, 2015 at 11:39 PM, Mishelle Oña 
> wrote:
> 
> > Yes, but I am not converting all the .trr file to gro I wanted to take
> > only one frame of the .trr and make it gro. That´s why my command is
> > trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro
> > if the command line above is wrong :( what is the command I should use for
> > taking out only one frame of a trajectory file in gro format
> > Mishelle
> >
> > > From: mark.j.abra...@gmail.com
> > > Date: Sun, 15 Nov 2015 22:06:38 +
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] Problems with trjconv
> > >
> > > Hi,
> > >
> > > Your question had one-word answer, which I gave!  :-) If the size of your
> > > files is worth thinking about, then converting them to gro format is not
> > a
> > > great idea.
> > >
> > > Mark
> > >
> > > On Sun, 15 Nov 2015 21:56 Mishelle Oña  wrote:
> > >
> > > > Eh, I don´t understand what you mean, please  explain me .Mishelle:)
> > > >
> > > > > From: mark.j.abra...@gmail.com
> > > > > Date: Sun, 15 Nov 2015 19:28:47 +
> > > > > To: gmx-us...@gromacs.org
> > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > >
> > > > > Hi,
> > > > >
> > > > > Certainly. You do not want to convert non-trivial trajectories to
> > text
> > > > > format.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña 
> > > > wrote:
> > > > >
> > > > > > well, I check and it is the same line of command. The biggest file
> > has
> > > > > > more weight than the .traj file and it is only a .gro file . Is
> > this
> > > > > > posible?
> > > > > > Mishelle
> > > > > > > From: mark.j.abra...@gmail.com
> > > > > > > Date: Sun, 15 Nov 2015 19:15:50 +
> > > > > > > To: gmx-us...@gromacs.org
> > > > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > Either you didn't issue the same command (inspect your terminal
> > > > history),
> > > > > > > or the second operation didn't complete (for any number of
> > reasons).
> > > > > > >
> > > > > > > Mark
> > > > > > >
> > > > > > > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña <
> > samimi...@hotmail.com>
> > > > > > wrote:
> > > > > > >
> > > > > > > > Hello, I have a question about trjconv. I have a .trr file and
> > I
> > > > put
> > > > > > the
> > > > > > > > following line of command: trjconv -f trajcentrada.trr -b 1646
> > -e
> > > > 1646
> > > > > > -o
> > > > > > > > 1646ps.gro I got back a file of 13813272703 bytes. Then I make
> > the
> > > > > > same and
> > > > > > > > got a file of 506444 bytes. Do you know what is
> > happening?Mishelle
> > > > > > > > --
> > > > > > > > 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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> > > > > > > > * 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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> > > > or
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> > > > > >
> > > > > > --
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> > > > > > posting!
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> > > > > >
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> > > > >
> > > 

Re: [gmx-users] restart issues with Gromacs

[Nash, Anthony]

Thanks Mark,

Ok, so it sounds very much like it¹s on the cluster side. I¹ll fire this
across to one of the sys admins and see if they can find out what the
problem is, although I have no idea what and if they will find anything.
>From the looks of it, the reading of the checkpoint file data was fine
(else I expect an MD5 hashkey error IF my memory serves me right).

Thanks again
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 15/11/2015 22:12, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
behalf of Mark Abraham"  wrote:

>Hi,
>
>GROMACS assumes the file systems actually write to disk when you use the
>system call that means that, and works correctly if so. But if the file
>system or its configuration don't actually do that (for "performance" or
>erroneous reasons), then all bets are off. mdrun can't even know if it's
>being lied to, because, well, it's being lied to...
>
>Mark
>
>On Sun, 15 Nov 2015 22:30 Nash, Anthony  wrote:
>
>> Hi all,
>>
>> Running Grimaces 5.0.4 with PLUMED 2.2 on a cluster, number of ranks
>>(MPI
>> processes) is 24. The simulation successfully ran for the maximum
>>cluster
>> wall time (48 hours).
>>
>> I attempt to restart the simulations using the following command (with a
>> sun microsystem grid engine submission script):
>>
>> gerun mdrun_mpi_d -deffnm neu_mut_meta_K -cpi neu_mut_meta_K.cpt
>>-noappend
>> -plumed
>>
>>
>> However, whilst the queue is telling me that the job is running, the
>> *.part0002.log file seems stuck at:
>>
>> ---
>> When dynamic load balancing gets turned on, these settings will change
>>to:
>> The maximum number of communication pulses is: X 1 Y 1
>> The minimum size for domain decomposition cells is 1.025 nm
>> The requested allowed shrink of DD cells (option -dds) is: 0.80
>> The allowed shrink of domain decomposition cells is: X 0.43 Y 0.56
>> The maximum allowed distance for charge groups involved in interactions
>>is:
>>  non-bonded interactions   1.025 nm
>> two-body bonded interactions  (-rdd)   1.025 nm
>>   multi-body bonded interactions  (-rdd)   1.025 nm
>>   atoms separated by up to 5 constraints  (-rcon)  1.025 nm
>> 
>>
>>
>> The cluster error file and output file (not gromacs file) contains no
>> warnings or errors. The gromacs log file contains no warnings or errors.
>>
>> I have seen this behaviour quite a number of times, going back to early
>> versions of gromacs 4 around late 2010 (I think). I got into the habit
>>of
>> a) copying backing up the .cpt files, and b) always using -noappend
>>option
>> to preserve the .trr file. Has there ever been an explanation as to why
>> this is happening?
>>
>> Many thanks
>> Anthony
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>-- 
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>posting!
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Re: [gmx-users] Problems with trjconv

[Mishelle Oña]

Yes, but I am not converting all the .trr file to gro I wanted to take only one 
frame of the .trr and make it gro. That´s why my command is  trjconv -f 
trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro
if the command line above is wrong :( what is the command I should use for 
taking out only one frame of a trajectory file in gro format
Mishelle

> From: mark.j.abra...@gmail.com
> Date: Sun, 15 Nov 2015 22:06:38 +
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problems with trjconv
> 
> Hi,
> 
> Your question had one-word answer, which I gave!  :-) If the size of your
> files is worth thinking about, then converting them to gro format is not a
> great idea.
> 
> Mark
> 
> On Sun, 15 Nov 2015 21:56 Mishelle Oña  wrote:
> 
> > Eh, I don´t understand what you mean, please  explain me .Mishelle:)
> >
> > > From: mark.j.abra...@gmail.com
> > > Date: Sun, 15 Nov 2015 19:28:47 +
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] Problems with trjconv
> > >
> > > Hi,
> > >
> > > Certainly. You do not want to convert non-trivial trajectories to text
> > > format.
> > >
> > > Mark
> > >
> > > On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña 
> > wrote:
> > >
> > > > well, I check and it is the same line of command. The biggest file has
> > > > more weight than the .traj file and it is only a .gro file . Is this
> > > > posible?
> > > > Mishelle
> > > > > From: mark.j.abra...@gmail.com
> > > > > Date: Sun, 15 Nov 2015 19:15:50 +
> > > > > To: gmx-us...@gromacs.org
> > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > >
> > > > > Hi,
> > > > >
> > > > > Either you didn't issue the same command (inspect your terminal
> > history),
> > > > > or the second operation didn't complete (for any number of reasons).
> > > > >
> > > > > Mark
> > > > >
> > > > > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña 
> > > > wrote:
> > > > >
> > > > > > Hello, I have a question about trjconv. I have a .trr file and I
> > put
> > > > the
> > > > > > following line of command: trjconv -f trajcentrada.trr -b 1646 -e
> > 1646
> > > > -o
> > > > > > 1646ps.gro I got back a file of 13813272703 bytes. Then I make the
> > > > same and
> > > > > > got a file of 506444 bytes. Do you know what is happening?Mishelle
> > > > > > --
> > > > > > 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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> > or
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> > > > > >
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Re: [gmx-users] Problems with trjconv

[Shantanu Maheshwari]

No it will not erase anything from .trr file.

On Mon, Nov 16, 2015 at 12:21 AM, Mishelle Oña 
wrote:

> Ok, but this erase the frame from my trajectory? because i don´t want to
> modify it.
>
> > Date: Mon, 16 Nov 2015 00:10:07 +0100
> > From: shantanu...@gmail.com
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Problems with trjconv
> >
> > If you want to take out only one frame then you can use -dump option.
> >
> > trjconv -f trajcentrada.trr -dump 1646 -o 1646ps.gro
> >
> > On Sun, Nov 15, 2015 at 11:39 PM, Mishelle Oña 
> > wrote:
> >
> > > Yes, but I am not converting all the .trr file to gro I wanted to take
> > > only one frame of the .trr and make it gro. That´s why my command is
> > > trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro
> > > if the command line above is wrong :( what is the command I should use
> for
> > > taking out only one frame of a trajectory file in gro format
> > > Mishelle
> > >
> > > > From: mark.j.abra...@gmail.com
> > > > Date: Sun, 15 Nov 2015 22:06:38 +
> > > > To: gmx-us...@gromacs.org
> > > > Subject: Re: [gmx-users] Problems with trjconv
> > > >
> > > > Hi,
> > > >
> > > > Your question had one-word answer, which I gave!  :-) If the size of
> your
> > > > files is worth thinking about, then converting them to gro format is
> not
> > > a
> > > > great idea.
> > > >
> > > > Mark
> > > >
> > > > On Sun, 15 Nov 2015 21:56 Mishelle Oña 
> wrote:
> > > >
> > > > > Eh, I don´t understand what you mean, please  explain me
> .Mishelle:)
> > > > >
> > > > > > From: mark.j.abra...@gmail.com
> > > > > > Date: Sun, 15 Nov 2015 19:28:47 +
> > > > > > To: gmx-us...@gromacs.org
> > > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > > >
> > > > > > Hi,
> > > > > >
> > > > > > Certainly. You do not want to convert non-trivial trajectories to
> > > text
> > > > > > format.
> > > > > >
> > > > > > Mark
> > > > > >
> > > > > > On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña <
> samimi...@hotmail.com>
> > > > > wrote:
> > > > > >
> > > > > > > well, I check and it is the same line of command. The biggest
> file
> > > has
> > > > > > > more weight than the .traj file and it is only a .gro file . Is
> > > this
> > > > > > > posible?
> > > > > > > Mishelle
> > > > > > > > From: mark.j.abra...@gmail.com
> > > > > > > > Date: Sun, 15 Nov 2015 19:15:50 +
> > > > > > > > To: gmx-us...@gromacs.org
> > > > > > > > Subject: Re: [gmx-users] Problems with trjconv
> > > > > > > >
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > Either you didn't issue the same command (inspect your
> terminal
> > > > > history),
> > > > > > > > or the second operation didn't complete (for any number of
> > > reasons).
> > > > > > > >
> > > > > > > > Mark
> > > > > > > >
> > > > > > > > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña <
> > > samimi...@hotmail.com>
> > > > > > > wrote:
> > > > > > > >
> > > > > > > > > Hello, I have a question about trjconv. I have a .trr file
> and
> > > I
> > > > > put
> > > > > > > the
> > > > > > > > > following line of command: trjconv -f trajcentrada.trr -b
> 1646
> > > -e
> > > > > 1646
> > > > > > > -o
> > > > > > > > > 1646ps.gro I got back a file of 13813272703 bytes. Then I
> make
> > > the
> > > > > > > same and
> > > > > > > > > got a file of 506444 bytes. Do you know what is
> > > happening?Mishelle
> > > > > > > > > --
> > > > > > > > > Gromacs Users mailing list
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> > > > > > > > > * Please search the archive at
> > > > > > > > >
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > > before
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> 

Re: [gmx-users] Problems with trjconv

[Mark Abraham]

Hi,

Your question had one-word answer, which I gave!  :-) If the size of your
files is worth thinking about, then converting them to gro format is not a
great idea.

Mark

On Sun, 15 Nov 2015 21:56 Mishelle Oña  wrote:

> Eh, I don´t understand what you mean, please  explain me .Mishelle:)
>
> > From: mark.j.abra...@gmail.com
> > Date: Sun, 15 Nov 2015 19:28:47 +
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Problems with trjconv
> >
> > Hi,
> >
> > Certainly. You do not want to convert non-trivial trajectories to text
> > format.
> >
> > Mark
> >
> > On Sun, Nov 15, 2015 at 8:20 PM Mishelle Oña 
> wrote:
> >
> > > well, I check and it is the same line of command. The biggest file has
> > > more weight than the .traj file and it is only a .gro file . Is this
> > > posible?
> > > Mishelle
> > > > From: mark.j.abra...@gmail.com
> > > > Date: Sun, 15 Nov 2015 19:15:50 +
> > > > To: gmx-us...@gromacs.org
> > > > Subject: Re: [gmx-users] Problems with trjconv
> > > >
> > > > Hi,
> > > >
> > > > Either you didn't issue the same command (inspect your terminal
> history),
> > > > or the second operation didn't complete (for any number of reasons).
> > > >
> > > > Mark
> > > >
> > > > On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña 
> > > wrote:
> > > >
> > > > > Hello, I have a question about trjconv. I have a .trr file and I
> put
> > > the
> > > > > following line of command: trjconv -f trajcentrada.trr -b 1646 -e
> 1646
> > > -o
> > > > > 1646ps.gro I got back a file of 13813272703 bytes. Then I make the
> > > same and
> > > > > got a file of 506444 bytes. Do you know what is happening?Mishelle
> > > > > --
> > > > > 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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> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
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> > > > >
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[gmx-users] Choosing LINCS setting / rcon for parallel mdrun

[Agnivo Gosai]

Dear Users,

I tried to do a NVT run on a cluster with -np = 64. My system size is 12405
atoms ( a protein in water )

I get the following error.

ERROR.

There is no domain decomposition for 56 nodes that is compatible with the
given box and a minimum cell size of 0.959375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings

8 nodes were assigned for PME cal by mdrun

This is the part of my NVT.mdp

; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.4  ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4  ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT

I would still like to use 64 processes for the mdrun. Any suggestions
please.

I am thinking of playing with -rcon. But I am not sure if it will affect
the accuracy of the simulation.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.
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Re: [gmx-users] Choosing LINCS setting / rcon for parallel mdrun

[Justin Lemkul]

On 11/15/15 8:09 PM, Agnivo Gosai wrote:

Dear Users,

I tried to do a NVT run on a cluster with -np = 64. My system size is 12405
atoms ( a protein in water )

I get the following error.

ERROR.

There is no domain decomposition for 56 nodes that is compatible with the
given box and a minimum cell size of 0.959375 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS
settings

8 nodes were assigned for PME cal by mdrun

This is the part of my NVT.mdp

; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.4  ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.4  ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT

I would still like to use 64 processes for the mdrun. Any suggestions
please.



Your system is too small to decompose over 64 cores.  One cannot arbitrarily 
parallelize any system over any number of cores/nodes.


-Justin


I am thinking of playing with -rcon. But I am not sure if it will affect
the accuracy of the simulation.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.



--
==

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

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

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

==
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[gmx-users] difference between entropic energy and free energy

[Ming Tang]

Deer list,

I am quite confused about the concept of entropic energy and free energy. Could 
anybody help to tell me what is the difference between them?

Thanks.
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[gmx-users] (no subject)

[Mehriar Amininasab]

Dear gromacs users,

Does anybody have an idea about the value of isothermal compressibility at 
kbar pressures.

yours,
Mehriar
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Re: [gmx-users] Problem with GROMACS simulation

[Peter Stern]

Dear Shantanu,

As Erik already told you, your attachments aren't accepted by the list so 
nobody can see them.
You need to download your files to some public place where everyone can access 
them if they want, e.g. Dropbox, etc.
Without looking at the relevant files, nobody can possibly help your with your 
problem, because nobody can see what it is.
Also, it would be much more useful to give a more descriptive "Subject" to you 
"problem" if you can.

Peter

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of 
Shantanu Singh
Sent: Sunday, November 15, 2015 7:20 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem with GROMACS simulation

How do i get help regarding my simulations?

I am working on an alkane system using TraPPE force field. There is some issue 
which I can't figure out how to solve.



On Sat, Nov 14, 2015 at 9:54 PM, Erik Marklund 
wrote:

> Hi,
>
> I don’t think attachments are accepted on the mailing list.
>
> Kind regards,
> Erik
>
> > On 14 Nov 2015, at 15:32, Shantanu Singh 
> wrote:
> >
> > Hello!
> >
> > I am a Senior undergraduate at IIT delhi, India. I have trying to
> simulate
> > a system of alkanes in water with the ultimate aim of determining 
> > their diffusion coefficients.
> >
> > So, when I'm trying to run a simulation, it gives an error. A copy 
> > of the error report has also been attached herein along with all 
> > other files involved in the simulation.
> >
> > I would be really grateful if you could find the time to take a look 
> > at them and help me out. This project is an essential part of my 
> > bachelors
> and
> > is very important to me.
> >
> >
> > Thank you.
> >
> > --
> > Regards
> >
> > Shantanu Singh
> > Senior Undergraduate
> > IIT Delhi
> > --
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--
Regards

Shantanu Singh
Senior Undergraduate
IIT Delhi
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Re: [gmx-users] Problem with GROMACS simulation

[Shantanu Singh]

How do i get help regarding my simulations?

I am working on an alkane system using TraPPE force field. There is some
issue which I can't figure out how to solve.



On Sat, Nov 14, 2015 at 9:54 PM, Erik Marklund 
wrote:

> Hi,
>
> I don’t think attachments are accepted on the mailing list.
>
> Kind regards,
> Erik
>
> > On 14 Nov 2015, at 15:32, Shantanu Singh 
> wrote:
> >
> > Hello!
> >
> > I am a Senior undergraduate at IIT delhi, India. I have trying to
> simulate
> > a system of alkanes in water with the ultimate aim of determining their
> > diffusion coefficients.
> >
> > So, when I'm trying to run a simulation, it gives an error. A copy of the
> > error report has also been attached herein along with all other files
> > involved in the simulation.
> >
> > I would be really grateful if you could find the time to take a look at
> > them and help me out. This project is an essential part of my bachelors
> and
> > is very important to me.
> >
> >
> > Thank you.
> >
> > --
> > Regards
> >
> > Shantanu Singh
> > Senior Undergraduate
> > IIT Delhi
> > --
> > 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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-- 
Regards

Shantanu Singh
Senior Undergraduate
IIT Delhi
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[gmx-users] gmx-us...@gromacs.org

[Mishelle Oña]

Hello, 
I have a question about trjconv. I have a .trr file and I put the following 
line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o 1646ps.gro I 
got back a file of 13813272703 bytes. Then I make the same and got a file of  
506444 bytes. Do you know what is happening?
Mishelle
  
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Re: [gmx-users] Problems with trjconv

[Mark Abraham]

Hi,

Either you didn't issue the same command (inspect your terminal history),
or the second operation didn't complete (for any number of reasons).

Mark

On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña  wrote:

> Hello, I have a question about trjconv. I have a .trr file and I put the
> following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o
> 1646ps.gro I got back a file of 13813272703 bytes. Then I make the same and
> got a file of 506444 bytes. Do you know what is happening?Mishelle
> --
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Re: [gmx-users] Problems with trjconv

[Mishelle Oña]

well, I check and it is the same line of command. The biggest file has more 
weight than the .traj file and it is only a .gro file . Is this posible?
Mishelle
> From: mark.j.abra...@gmail.com
> Date: Sun, 15 Nov 2015 19:15:50 +
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problems with trjconv
> 
> Hi,
> 
> Either you didn't issue the same command (inspect your terminal history),
> or the second operation didn't complete (for any number of reasons).
> 
> Mark
> 
> On Sun, Nov 15, 2015 at 8:13 PM Mishelle Oña  wrote:
> 
> > Hello, I have a question about trjconv. I have a .trr file and I put the
> > following line of command: trjconv -f trajcentrada.trr -b 1646 -e 1646 -o
> > 1646ps.gro I got back a file of 13813272703 bytes. Then I make the same and
> > got a file of 506444 bytes. Do you know what is happening?Mishelle
> > --
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> >
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