date:20180417

Re: [gmx-users] Error in gmx trjcat

2018-04-17 Thread Syed Azeem

>> Hey Mark,
>>
>> Still the same problem persists.
>>
>>
>>
> Hi,
>
> That looks like a broken build of GROMACS, rather than a bug in the code or
> a broken file. Can you try those gmx check commands on another installation
> somewhere else? (Also gmx check -m doesn't do anything useful any more, so
> don't buy trouble by using it!)

Hey,

I tried concatenating those trajectory files in another machine (same
version: gromacs 5.1.4). It worked well without any error.

What is wrong with my own build?

Best,
Azeem
>
> Mark
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[gmx-users] Length of a constrained bond

2018-04-17 Thread Eric Smoll

Hello Gromacs Users,

When setting "constraints=h-bonds" in an mdp file, what sets the
constrained bond length? Is it the equilibrium bond length in the topology,
the bond length deduced from the initial coordinates, or something else.

Best,
Eric
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[gmx-users] simulation crash

2018-04-17 Thread Andrea Spitaleri


Hi there,

I am running several independent replica of similar system but in 
different pose of protein-peptide. I am in NVT ensemble and the length 
of the simulation is 125ns (dt=2fs). Few of them are crashing with the 
classic error:


"1 particles communicated to PME node 8 are more than 2/3 times the 
cut-off out of the domain decomposition cell of their charge group in 
dimension x.

This usually means that your system is not well equilibrated."

I am using 36 cores or a multiple of 36 (i.e. 72, 108, and so on). The 
weird things is that restarting the crashed replica from the checkpoint, 
it starts without problem and it goes for a while (hours). Then it 
crashes again and so on. I have checked the last frame before the crash 
and I do not see structural problem. Changing the number of cores from 1 
to 5 improves the things but not too much, it still crashes and 
restarts. IMHO, if there was a problem with the system the simulation 
should never restart, isn't?


any clue?

Hope I have been clear

Best

Andrea


--
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
http://it.linkedin.com/in/andreaspitaleri
https://www.researchgate.net/profile/Andrea_Spitaleri
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ORCID: http://orcid.org/-0003-3012-3557

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[gmx-users] 3dc warning

2018-04-17 Thread Eric Smoll

Hello Gromacs users,

I am using version 2018.1.

I have a system in an infinite slab configuration (periodic in the x and y
dimensions; in the z dimension, the atoms are permanently confined to 1/3
of the unit cell length with the remainder vacuum).

I am interested in simulating the system with 3D PBC and PME. Since I am
only interested in the behavior of a single infinite slab, interactions
between images of the slab in the z-dimension are unwanted. The 3dc
correction seems like a useful way to increase the realism in my
simulations.

However, grompp generates a warning: "With PME and ewald_geometry = 3dc you
should use pbc = xy"

As I understand it, 3dc is a correction for periodicity in the z-dimension.
Is pbc=xyz inappropriate?

Best,
Eric
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Re: [gmx-users] trjconv ndec not working

2018-04-17 Thread Eric Smoll

Paul and Mark,

Thanks for the reply! Good to know I wasn't doing anything wrong.

Best,
Eric

On Tue, Apr 17, 2018 at 10:08 AM, Mark Abraham 
wrote:

> Hi,
>
> What Paul said agrees with my memory, but I'd not found time to check that
> yet. We should indeed fix the docs.
>
> Mark
>
> On Tue, Apr 17, 2018, 16:42 Paul Bauer  wrote:
>
> > Hello Eric,
> >
> > I had a look at the code for writing gro files and it looks to me that
> > it is only able to write three decimal places there.
> > There is a comment in the code that mentions that writing other
> > precisions has been removed.
> > This means that we need to update the man page text to not be confusing.
> >
> > Cheers
> >
> > Paul
> >
> >
> > On 2018-04-15 17:45, Eric Smoll wrote:
> > > Hello Joe,
> > >
> > > Thanks for the reply. Sorry if I was not clear. I provide a gro file
> > with high precision (7 decimal places). For some reason, the output gro
> > always has three decimal places. The manual   for trjconv suggests that
> the
> > output should have 7 decimal places.
> > >
> > > Best,
> > > Eric
> > >
> > >> On Apr 15, 2018, at 4:00 AM, Joe Jordan 
> wrote:
> > >>
> > >> Are you trying to write from an xtc file? If so, does it have the
> > necessary
> > >> precision?
> > >>
> > >>> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll 
> > wrote:
> > >>>
> > >>> Hello Gromacs Users,
> > >>>
> > >>> I am using Gromacs 2018.1.
> > >>>
> > >>> The manual page for gmx trjconv states the number of decimal places
> in
> > the
> > >>> output of a gro file is taken from the number of decimal places in
> the
> > >>> input unless the ndec flag is set. The ndec flag can be used to
> > increase
> > >>> precision in the output.
> > >>>
> > >>> However, providing trjconv a gro file with increased coordinate
> > precision
> > >>> (7 decimal places) does not increase the precision of the output gro
> > file.
> > >>> Also, the ndec flag has no impact on the output precision.
> > >>>
> > >>> My input gro is written as follows:
> > >>>
> > >>> comment
> > >>> 10
> > >>> 1ABC C11  -0.1204914  -0.0759159  -0.0131147
> > >>> ...etc.
> > >>>
> > >>> trconv does not complain about this file format and creates a normal,
> > three
> > >>> decimal
> > >>> gro file as output.
> > >>>
> > >>> Has this feature been removed?
> > >>>
> > >>> Best,
> > >>> Eric
> > >>> --
> > >>> 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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> or
> > >>> send a mail to gmx-users-requ...@gromacs.org.
> > >>>
> > >>
> > >>
> > >> --
> > >> Joe Jordan
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
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> > posting!
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> >
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Re: [gmx-users] trjconv ndec not working

2018-04-17 Thread Mark Abraham

Hi,

What Paul said agrees with my memory, but I'd not found time to check that
yet. We should indeed fix the docs.

Mark

On Tue, Apr 17, 2018, 16:42 Paul Bauer  wrote:

> Hello Eric,
>
> I had a look at the code for writing gro files and it looks to me that
> it is only able to write three decimal places there.
> There is a comment in the code that mentions that writing other
> precisions has been removed.
> This means that we need to update the man page text to not be confusing.
>
> Cheers
>
> Paul
>
>
> On 2018-04-15 17:45, Eric Smoll wrote:
> > Hello Joe,
> >
> > Thanks for the reply. Sorry if I was not clear. I provide a gro file
> with high precision (7 decimal places). For some reason, the output gro
> always has three decimal places. The manual   for trjconv suggests that the
> output should have 7 decimal places.
> >
> > Best,
> > Eric
> >
> >> On Apr 15, 2018, at 4:00 AM, Joe Jordan  wrote:
> >>
> >> Are you trying to write from an xtc file? If so, does it have the
> necessary
> >> precision?
> >>
> >>> On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll 
> wrote:
> >>>
> >>> Hello Gromacs Users,
> >>>
> >>> I am using Gromacs 2018.1.
> >>>
> >>> The manual page for gmx trjconv states the number of decimal places in
> the
> >>> output of a gro file is taken from the number of decimal places in the
> >>> input unless the ndec flag is set. The ndec flag can be used to
> increase
> >>> precision in the output.
> >>>
> >>> However, providing trjconv a gro file with increased coordinate
> precision
> >>> (7 decimal places) does not increase the precision of the output gro
> file.
> >>> Also, the ndec flag has no impact on the output precision.
> >>>
> >>> My input gro is written as follows:
> >>>
> >>> comment
> >>> 10
> >>> 1ABC C11  -0.1204914  -0.0759159  -0.0131147
> >>> ...etc.
> >>>
> >>> trconv does not complain about this file format and creates a normal,
> three
> >>> decimal
> >>> gro file as output.
> >>>
> >>> Has this feature been removed?
> >>>
> >>> Best,
> >>> Eric
> >>> --
> >>> 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.
> >>>
> >>
> >>
> >> --
> >> Joe Jordan
> >> --
> >> Gromacs Users mailing list
> >>
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Re: [gmx-users] trjconv ndec not working

2018-04-17 Thread Paul Bauer


Hello Eric,

I had a look at the code for writing gro files and it looks to me that 
it is only able to write three decimal places there.
There is a comment in the code that mentions that writing other 
precisions has been removed.

This means that we need to update the man page text to not be confusing.

Cheers

Paul


On 2018-04-15 17:45, Eric Smoll wrote:

Hello Joe,

Thanks for the reply. Sorry if I was not clear. I provide a gro file with high 
precision (7 decimal places). For some reason, the output gro always has three 
decimal places. The manual   for trjconv suggests that the output should have 7 
decimal places.

Best,
Eric


On Apr 15, 2018, at 4:00 AM, Joe Jordan  wrote:

Are you trying to write from an xtc file? If so, does it have the necessary
precision?


On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll  wrote:

Hello Gromacs Users,

I am using Gromacs 2018.1.

The manual page for gmx trjconv states the number of decimal places in the
output of a gro file is taken from the number of decimal places in the
input unless the ndec flag is set. The ndec flag can be used to increase
precision in the output.

However, providing trjconv a gro file with increased coordinate precision
(7 decimal places) does not increase the precision of the output gro file.
Also, the ndec flag has no impact on the output precision.

My input gro is written as follows:

comment
10
1ABC C11  -0.1204914  -0.0759159  -0.0131147
...etc.

trconv does not complain about this file format and creates a normal, three
decimal
gro file as output.

Has this feature been removed?

Best,
Eric
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Re: [gmx-users] CGenff parameters in gromacs but missing in charmm package

2018-04-17 Thread Justin Lemkul

On 4/17/18 11:24 AM, Fabian Keller wrote:

Dear Justin,

On 4/17/18 3:34 AM, Fabian Keller wrote:

Dear all,
I am using the CGenFF/paramchem framework for a new molecule (an imidazolium
cation derivative with methyl groups on both N atoms).
I faced a known problem going from CHARMM package to Gromacs with parameters
already existing in CHARMM for Gromacs. I assume that this is due to paramchem
only being implemented for CGenFF3.0.1 and Gromacs using version 4.1.

That's precisely your problem. The CGenFF server is using an old
version, and therefore it finds bonded parameters that need to be
guessed by analogy. In fact, CGenFF 4.0 has these parameters and they
are the values you should use. So for all of the parameters that are
being overridden, remove them from your .prm file before #including it
in the topology. The optimized parameters in CGenFF 4.0 are what you
want, and they're all already there in ffbonded.itp.

Okay thanks, this is what I did. I just was not sure wether the approach was
appropriate.

I wanted now to check if the parameters exist in the CGenFF for CHARMM and they
don?t!

I'm finding them. It's impossible for grompp to say something is in
ffbonded.itp if it isn't. Be sure you're considering forward and reverse
orders of atom types when you're searching for them.

Yes, sure you find them in the charmm36-jul2017.ff/ffbonded.itp, but they are
missing in the CGenFF version for CHARMM the
toppar_c36_jul17/par_all36_cgenff.prm file (both the latest release). So why is
there a discrepancy, or is it even a discrepancy or rather something I am
missing here?

The GROMACS files come directly from the CHARMM files via a Python
script. There's no secret magic. If it's in GROMACS, it's in CHARMM.
You're either looking in the wrong place or you're trying to match the
wrong string.

-Justin

How is it possible that the parameters exist in the Gromacs version of CHARMM force-field
(http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz

)
while they are missing in the CHARMM FF version
(http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz

)?
Why are the dihedrals considered duplicate, when the atomtypes clearly are
different? Is this due to CHARMM handling dihedral potentials differently to
Gromacs?

Following the link you find all used parameter and force field files
(https://www.dropbox.com/sh/m89q64g0pae6wrf/AAAx1aNtJ1TZKNDFgUo2oSu7a?dl=0
)
and in the following the error output.
Thank you very much for all hints and help!
Best wishes,
Fabian

WARNING 1 [file chim.prm, line 4]:
Overriding Bond parameters.

old: 0.1468 276144 0.1468 276144
new: CG334 NG2R52 1 0.1453251040.00

WARNING 2 [file chim.prm, line 11]:
Overriding U-B parameters.

old: 107 351.456 0 0 107 351.456 0 0
new: NG2R52CG334 HGA3 5 110.10 351.456000 0.
0.00

WARNING 3 [file chim.prm, line 13]:
Overriding U-B parameters.

old: 126.3 368.192 0.243 19246.4
126.3 368.192 0.243 19246.4
new: CG2R53 NG2R52CG334 5 127.10 209.20 0.2090
12552.00

ERROR 1 [file chim.prm, line 25]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

ERROR 2 [file chim.prm, line 26]:
Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported.

Thanks a lot,
Fabian

--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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Blacksburg, VA 24061

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Re: [gmx-users] CGenff parameters in gromacs but missing in charmm package

2018-04-17 Thread Fabian Keller

Dear Justin,

> On 4/17/18 3:34 AM, Fabian Keller wrote:
>> Dear all,
>> I am using the CGenFF/paramchem framework for a new molecule (an imidazolium 
>> cation derivative with methyl groups on both N atoms).
>> I faced a known problem going from CHARMM package to Gromacs with parameters 
>> already existing in CHARMM for Gromacs. I assume that this is due to 
>> paramchem only being implemented for CGenFF3.0.1 and Gromacs using version 
>> 4.1.
> 
> That's precisely your problem. The CGenFF server is using an old 
> version, and therefore it finds bonded parameters that need to be 
> guessed by analogy. In fact, CGenFF 4.0 has these parameters and they 
> are the values you should use. So for all of the parameters that are 
> being overridden, remove them from your .prm file before #including it 
> in the topology. The optimized parameters in CGenFF 4.0 are what you 
> want, and they're all already there in ffbonded.itp.

Okay thanks, this is what I did. I just was not sure wether the approach was 
appropriate.


>> I wanted now to check if the parameters exist in the CGenFF for CHARMM and 
>> they don?t!
> 
> I'm finding them. It's impossible for grompp to say something is in 
> ffbonded.itp if it isn't. Be sure you're considering forward and reverse 
> orders of atom types when you're searching for them.

Yes, sure you find them in the charmm36-jul2017.ff/ffbonded.itp, but they are 
missing in the CGenFF version for CHARMM the 
toppar_c36_jul17/par_all36_cgenff.prm file (both the latest release). So why is 
there a discrepancy, or is it even a discrepancy or rather something I am 
missing here?


> 
>> How is it possible that the parameters exist in the Gromacs version of 
>> CHARMM force-field 
>> (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2017.ff.tgz
>>  
>> )
>>  while they are missing in the CHARMM FF version 
>> (http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_jul17.tgz
>>  
>> )?
>> Why are the dihedrals considered duplicate, when the atomtypes clearly are 
>> different? Is this due to CHARMM handling dihedral potentials differently to 
>> Gromacs?
>> 
>> Following the link you find all used parameter and force field files 
>> (https://www.dropbox.com/sh/m89q64g0pae6wrf/AAAx1aNtJ1TZKNDFgUo2oSu7a?dl=0 
>> ) 
>> and in the following the error output.
>> Thank you very much for all hints and help!
>> Best wishes,
>> Fabian
>> 
>> 
>> 
>> 
>> 
>> 
>> WARNING 1 [file chim.prm, line 4]:
>>   Overriding Bond parameters.
>> 
>>   old:  0.1468 276144 0.1468 276144
>>   new: CG334   NG2R52 1   0.1453251040.00
>> 
>> 
>> WARNING 2 [file chim.prm, line 11]:
>>   Overriding U-B parameters.
>> 
>>   old:  107 351.456 0 0 107 351.456 
>> 0 0
>>   new: NG2R52CG334 HGA3 5   110.10   351.456000   0. 
>> 0.00
>> 
>> 
>> WARNING 3 [file chim.prm, line 13]:
>>   Overriding U-B parameters.
>> 
>>   old:  126.3 368.192 0.243 19246.4 
>> 126.3 368.192 0.243 19246.4
>>   new: CG2R53   NG2R52CG334 5   127.10   209.20   0.2090 
>> 12552.00
>> 
>> 
>> ERROR 1 [file chim.prm, line 25]:
>>   Encountered a second block of parameters for dihedral type 9 for the same
>>   atoms, with either different parameters and/or the first block has
>>   multiple lines. This is not supported.
>> 
>> 
>> ERROR 2 [file chim.prm, line 26]:
>>   Encountered a second block of parameters for dihedral type 9 for the same
>>   atoms, with either different parameters and/or the first block has
>>   multiple lines. This is not supported.


Thanks a lot,
Fabian
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Re: [gmx-users] Error in gmx trjcat

2018-04-17 Thread Mark Abraham

On Tue, Apr 17, 2018 at 3:32 PM Syed Azeem 
wrote:

> Hey Mark,
>
> Still the same problem persists.
>
>
>
Hi,

That looks like a broken build of GROMACS, rather than a bug in the code or
a broken file. Can you try those gmx check commands on another installation
somewhere else? (Also gmx check -m doesn't do anything useful any more, so
don't buy trouble by using it!)

Mark
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Re: [gmx-users] Error in gmx trjcat

2018-04-17 Thread Syed Azeem

Hey Mark,

Still the same problem persists.

GROMACS:  gmx check, VERSION 5.1.4
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx check -f new2.xtc -m report.tex

Checking file new2.xtc
Reading frame   0 time 10.000
# Atoms  10174
Precision 0.001 (nm)
Reading frame8000 time 18.000   *** Error in `gmx':
munmap_chunk(): invalid pointer: 0x021a5680 ***
=== Backtrace: =
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fa4f0d337e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7fa4f0d40698]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(xdr3dfcoord+0x1387)[0x7fa4f1d461d7]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_xtc+0x1bd)[0x7fa4f1d6839d]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(read_next_frame+0x267)[0x7fa4f1d64977]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(chk_trj+0x58d)[0x7fa4f20bb19d]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(gmx_check+0x2da)[0x7fa4f20be56a]
/usr/local/gromacs/bin/../lib/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x334)[0x7fa4f1add4c4]
gmx(main+0x8c)[0x40c98c]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fa4f0cdc830]
gmx(_start+0x29)[0x40cb19]
=== Memory map: 
0040-0043d000 r-xp  08:07 2646598
  /usr/local/gromacs/bin/gmx
0063c000-0063d000 r--p 0003c000 08:07 2646598
  /usr/local/gromacs/bin/gmx
0063d000-0063e000 rw-p 0003d000 08:07 2646598
  /usr/local/gromacs/bin/gmx
0063e000-0063f000 rw-p  00:00 0
02167000-02207000 rw-p  00:00 0  [heap]
7fa4f0471000-7fa4f0492000 r-xp  08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0492000-7fa4f0691000 ---p 00021000 08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0691000-7fa4f0692000 r--p 0002 08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0692000-7fa4f0693000 rw-p 00021000 08:07 2098798
  /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7fa4f0693000-7fa4f06ab000 r-xp  08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f06ab000-7fa4f08aa000 ---p 00018000 08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f08aa000-7fa4f08ab000 r--p 00017000 08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f08ab000-7fa4f08ac000 rw-p 00018000 08:07 2623397
  /lib/x86_64-linux-gnu/libpthread-2.23.so
7fa4f08ac000-7fa4f08b rw-p  00:00 0
7fa4f08b-7fa4f08b7000 r-xp  08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7fa4f08b7000-7fa4f0ab6000 ---p 7000 08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7fa4f0ab6000-7fa4f0ab7000 r--p 6000 08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7fa4f0ab7000-7fa4f0ab8000 rw-p 7000 08:07 2639498
  /lib/x86_64-linux-gnu/librt-2.23.so
7fa4f0ab8000-7fa4f0abb000 r-xp  08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0abb000-7fa4f0cba000 ---p 3000 08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0cba000-7fa4f0cbb000 r--p 2000 08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0cbb000-7fa4f0cbc000 rw-p 3000 08:07 2623462
  /lib/x86_64-linux-gnu/libdl-2.23.so
7fa4f0cbc000-7fa4f0e7c000 r-xp  08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7fa4f0e7c000-7fa4f107c000 ---p 001c 08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7fa4f107c000-7fa4f108 r--p 001c 08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7fa4f108-7fa4f1082000 rw-p 001c4000 08:07 2623402
  /lib/x86_64-linux-gnu/libc-2.23.so
7fa4f1082000-7fa4f1086000 rw-p  00:00 0
7fa4f1086000-7fa4f109c000 r-xp  08:07 2626206
  /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4f109c000-7fa4f129b000 ---p 00016000 08:07 2626206
  /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4f129b000-7fa4f129c000 rw-p 00015000 08:07 2626206
  /lib/x86_64-linux-gnu/libgcc_s.so.1
7fa4f129c000-7fa4f13a4000 r-xp  08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7fa4f13a4000-7fa4f15a3000 ---p 00108000 08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7fa4f15a3000-7fa4f15a4000 r--p 00107000 08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7fa4f15a4000-7fa4f15a5000 rw-p 00108000 08:07 2621457
  /lib/x86_64-linux-gnu/libm-2.23.so
7fa4f15a5000-7fa4f1717000 r-xp  08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1717000-7fa4f1917000 ---p 00172000 08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1917000-7fa4f1921000 r--p 00172000 08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1921000-7fa4f1923000 rw-p 0017c000 08:07 2100941
  /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7fa4f1923000-7fa4f1927000 rw-p  00:00 0
7fa4f1927000-7fa4f2c74000 r-xp  08:07 2646399
  /usr/local/gromacs/lib/libgromacs.so.1.4.0
7fa4f2c74000-7fa4f2e73000 ---p 0134d000 08:07 2646399
  /usr/local/gromacs/lib/libgromacs.so.1.4.0
7fa4f2e73000-7fa4f2e92000 r--p 0134c000 08:07 2646399
  /usr/local/gromacs/lib/libgromacs.so.1.4.0
7fa4f2e92000-7fa4f2eb4000 rw-p

Re: [gmx-users] CGenff parameters in gromacs but missing in charmm package

2018-04-17 Thread Justin Lemkul

On 4/17/18 3:34 AM, Fabian Keller wrote:

I wanted now to check if the parameters exist in the CGenFF for CHARMM and they
don’t!