Re: [gmx-users] Chain length of a polymer

[Alessandra Villa]

Hi,

I  understood, that you would like to monitor the distance between the two
ends of your chains along the simulation. If this is the  case
 you could use
gmx distance (see
http://manual.gromacs.org/current/onlinehelp/gmx-distance.html) together
with the appropriate selection (e.i. you could calculate the distance
between the com of the two polymer ends)
In alternative you can use gmx mindist (
http://manual.gromacs.org/2019/onlinehelp/gmx-mindist.html)

To generate index files you can use gmx make_ndx (
http://manual.gromacs.org/2019/onlinehelp/gmx-make_ndx.html)

Best regards
Alessandra

On Thu, Nov 21, 2019 at 1:40 AM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Gromacs Users,
>
> I have a polymer molecule in my MD simulation and I want to calculate how
> chain length varies with simulation time. How can I do that with Gromacs
> software? Can I use gmx distance? Do I need to create a group with backbone
> atoms of the polymer chain in the index file for the calculation?
> Appreciate your help.
>
> Thank you.
> --
> Best Regards
> Shan Jayasinghe
> --
> Gromacs Users mailing list
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Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

[Justin Lemkul]

On 11/20/19 8:51 PM, Mijiddorj B wrote:

Dear Prof. Justin,

Thank you very much for your reply. I would like to use charmm27 because my
system contains a surface model, which were parametrized by INTERFACE Force
Field and compatible with charmm27. The polymer parameters of charmm27 were


AFAIK there's no reason to believe you have to use CHARMM27; INTERFACE 
is generally compatible with CHARMM, which has a linear development 
history so you should be able to combine it with any CHARMM potential.



generated by swissparam, and the server renamed the atomtypes. I would like
to assign those parameters with original charmm27. If possible, I would
like to use original charmm27 parameters instead of the values of
swissparam. I used charmm36 atomtypes for clarification.
I do not know the atom type of the nitrogen which connected with three
carbons.


NG301. I still think it's best if you simply parametrize your monomer 
units with CGenFF and use its parameters unless there are major penalties.


-Justin



Best regards,

Mijiddorj

--

Message: 5
Date: Wed, 20 Nov 2019 20:19:16 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
 for polymer
Message-ID: <7db2548d-f487-a34b-f27f-0f876aa20...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 11/19/19 9:54 PM, Mijiddorj B wrote:

Dear Gmx users,

Currently, I am trying to assign the atomtypes in charmm27 for the
polyethyleneimine polymer. It includes several different groups of

atoms. I

included following illustration and asignment:
##
   H CH2
   | /
NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...

##
I assigned and the charmm27 atomtypes as following and compared charmm36
atomtypes generated by CgenFF.
Atom   Charmm27 Charmm36
N (NH2) ---> NH2   |NG321
N (NH1) ---> NH1   |NG311
C (CH2) ---> CT2   |CG321
H (HC2) ---> HA |HGA2
N ?   |NG301

If you have any experience, please check my assignments the charmm27 atom
types and advice me the atomtype of the last Nitrogen, which were

assigned

as NG301 with CgenFF.

Why are you replacing the CGenFF atom types? The replacements you are
making completely change the LJ terms and therefore render the dihedral
parameters invalid. There is no need to make these changes, just use the
CGenFF atom types in your simulation (all of which is contained in the
CHARMM36 port, which you should use rather than the outdated CHARMM27
force field files).

-Justin

--
==

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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End of gromacs.org_gmx-users Digest, Vol 187, Issue 49
**



--
==

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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[gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer

[Mijiddorj B]

Dear Prof. Justin,

Thank you very much for your reply. I would like to use charmm27 because my
system contains a surface model, which were parametrized by INTERFACE Force
Field and compatible with charmm27. The polymer parameters of charmm27 were
generated by swissparam, and the server renamed the atomtypes. I would like
to assign those parameters with original charmm27. If possible, I would
like to use original charmm27 parameters instead of the values of
swissparam. I used charmm36 atomtypes for clarification.
I do not know the atom type of the nitrogen which connected with three
carbons.

Best regards,

Mijiddorj

--
>
> Message: 5
> Date: Wed, 20 Nov 2019 20:19:16 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments
> for polymer
> Message-ID: <7db2548d-f487-a34b-f27f-0f876aa20...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/19/19 9:54 PM, Mijiddorj B wrote:
> > Dear Gmx users,
> >
> > Currently, I am trying to assign the atomtypes in charmm27 for the
> > polyethyleneimine polymer. It includes several different groups of
> atoms. I
> > included following illustration and asignment:
> > ##
> >   H CH2
> >   | /
> > NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...
> >
> > ##
> > I assigned and the charmm27 atomtypes as following and compared charmm36
> > atomtypes generated by CgenFF.
> > Atom   Charmm27 Charmm36
> > N (NH2) ---> NH2   |NG321
> > N (NH1) ---> NH1   |NG311
> > C (CH2) ---> CT2   |CG321
> > H (HC2) ---> HA |HGA2
> > N ?   |NG301
> >
> > If you have any experience, please check my assignments the charmm27 atom
> > types and advice me the atomtype of the last Nitrogen, which were
> assigned
> > as NG301 with CgenFF.
>
> Why are you replacing the CGenFF atom types? The replacements you are
> making completely change the LJ terms and therefore render the dihedral
> parameters invalid. There is no need to make these changes, just use the
> CGenFF atom types in your simulation (all of which is contained in the
> CHARMM36 port, which you should use rather than the outdated CHARMM27
> force field files).
>
> -Justin
>
> --
> ==
>
> 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
>
> ==
>
>
>
> --
>
> --
> 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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>
> End of gromacs.org_gmx-users Digest, Vol 187, Issue 49
> **
>
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Re: [gmx-users] How to prepare prm and itp files of ligands from gro and top files prepared with Gauss, ambertool and acpye for gromacs simulations

[Justin Lemkul]

On 11/20/19 4:49 AM, Sun Yeping wrote:

Dear everyone,

In order to perform gromacs simulations with ligand-protein complex, I have
to prepare the force field files for the ligand.
I first use Gauss to generate a Lig.gesp file which describe the
electrostatic potential. Then I use antechamber  from ambertool to fit the
gesp charges and generate a lig.mol2 file.

   antechamber -i Lig.gesp -fi gesp -o Lig.mol2 -fo mol2 -pf y -c resp

After that, I use parmchk2 to generate the frcmod file

   parmchk2 -i Lig.mol2 -f mol2 -o Lig.frcmod

Then the Lig.inpcrd coordinate file is prepared by tleap program from
ambertool, following which I use the acpye the generate the top and gro
files.

  acpype -p Lig.prmtop -x Lig.inpcrd -d

Now I have Lig.gro and Lig.top files in hand. However, to perform gromacs
simulation, I need the .prm and .itp files. Could you tell me how to get
these files?


You already have what you need - coordinates and topology. A .top is the 
same as .itp except that it defines a system. It should already have all 
the parameters (if needed) and [moleculetype] definition of the ligand. 
Just remove any #include statements to other force field files and any 
[system] or [molecules] directives and it is an .itp that you can use 
directly.


-Justin

--
==

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] Charmm27 and Charmm36 atomtypes assignments for polymer

[Justin Lemkul]

On 11/19/19 9:54 PM, Mijiddorj B wrote:

Dear Gmx users,

Currently, I am trying to assign the atomtypes in charmm27 for the
polyethyleneimine polymer. It includes several different groups of atoms. I
included following illustration and asignment:
##
  H CH2
  | /
NH2--CH2--CH2--N--CH2--CH2--N--CH2 ...

##
I assigned and the charmm27 atomtypes as following and compared charmm36
atomtypes generated by CgenFF.
Atom   Charmm27 Charmm36
N (NH2) ---> NH2   |NG321
N (NH1) ---> NH1   |NG311
C (CH2) ---> CT2   |CG321
H (HC2) ---> HA |HGA2
N ?   |NG301

If you have any experience, please check my assignments the charmm27 atom
types and advice me the atomtype of the last Nitrogen, which were assigned
as NG301 with CgenFF.


Why are you replacing the CGenFF atom types? The replacements you are 
making completely change the LJ terms and therefore render the dihedral 
parameters invalid. There is no need to make these changes, just use the 
CGenFF atom types in your simulation (all of which is contained in the 
CHARMM36 port, which you should use rather than the outdated CHARMM27 
force field files).


-Justin

--
==

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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[gmx-users] Chain length of a polymer

[Shan Jayasinghe]

Dear Gromacs Users,

I have a polymer molecule in my MD simulation and I want to calculate how
chain length varies with simulation time. How can I do that with Gromacs
software? Can I use gmx distance? Do I need to create a group with backbone
atoms of the polymer chain in the index file for the calculation?
Appreciate your help.

Thank you.
-- 
Best Regards
Shan Jayasinghe
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Re: [gmx-users] replica exchange with GROMACS

[David de Sancho]

Hi
If I may answer your question, you are missing the name of your run input
file, which should be inside each of these directories. So in case you have
the set of tpr files and they are clalled run.tpr in the correct location,
adding -s run.tpr to the command should do the trick. You can find more
instructions here
http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html
All the best,

David

On Wed, 20 Nov 2019 at 16:35, hind ahmed  wrote:

>
> Hello
> Could you please direct me to how  can I run job of  replica exchange
> with GROMACS.  I used the setting bellow to submit the job on HEC, the job
> works but with no replex exchange and i got the note below.
> #run the md
> Mpirun -np 16 mdrun_mpi_d -multidir rep_0 rep_1 rep_2  rep_3  rep_4
> rep_5  rep_6  rep_7  rep_8  rep_9  rep_10 rep_11 rep_12 rep_13  rep_14
> rep_15 -replex 100
> Is there any guide to how i run it right?
>
> NOTE: The number of threads is not equal to the number of (logical) cores
>
>   and the -pin option is set to auto: will not pin thread to cores.
>   This can lead to significant performance degradation.
>   Consider using -pin on (and -pinoffset in case you run multiple
> jobs).
>
>
> Tthanks
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>


-- 
David De Sancho 
Ramón y Cajal Fellow (UPV/EHU)
Donostia International Physics Center
Manuel Lardizabal Ibilbidea, 4
20018 San Sebastian, Spain
Tel: +34 943018527
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[gmx-users] multidir, Segmentation fault

[Tamas Hegedus]

Hi,

I ran two equilibration simulations to generate two production tpr with 
different velocities.

mdrun_mpi runs fine with each tpr (no explosion, the systems are stable).
However, if I set the multidir option, I get segmentation fault.
My system: Debian Buster, GROMACS 2018.6

Thanks for your suggestions,
Tamas

[myhost:39226] Signal: Segmentation fault (11)
[myhost:39226] Signal code: Address not mapped (1)
[myhost:39226] Failing at address: 0x7f94b42e0008
[myhost:39226] [ 0] 
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12730)[0x7f94ab991730]
[myhost:39226] [ 1] 
/usr/lib/x86_64-linux-gnu/pmix/lib/pmix/mca_gds_ds21.so(+0x2936)[0x7f94a9f72936]
[myhost:39226] [ 2] 
/usr/lib/x86_64-linux-gnu/libmca_common_dstore.so.1(pmix_common_dstor_init+0x9d3)[0x7f94a9f62733]
[myhost:39226] [ 3] 
/usr/lib/x86_64-linux-gnu/pmix/lib/pmix/mca_gds_ds21.so(+0x25b4)[0x7f94a9f725b4]
[myhost:39226] [ 4] 
/usr/lib/x86_64-linux-gnu/libpmix.so.2(pmix_gds_base_select+0x12e)[0x7f94aa0a946e]
[myhost:39226] [ 5] 
/usr/lib/x86_64-linux-gnu/libpmix.so.2(pmix_rte_init+0x8cd)[0x7f94aa06188d]
[myhost:39226] [ 6] 
/usr/lib/x86_64-linux-gnu/libpmix.so.2(PMIx_Init+0xdc)[0x7f94aa01dd7c]
[myhost:39226] [ 7] 
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_pmix_ext2x.so(ext2x_client_init+0xc4)[0x7f94aa113fe4]
[myhost:39226] [ 8] 
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_ess_pmi.so(+0x2656)[0x7f94aade3656]
[myhost:39226] [ 9] 
/usr/lib/x86_64-linux-gnu/libopen-rte.so.40(orte_init+0x29a)[0x7f94aaedc11a]
[myhost:39226] [10] 
/usr/lib/x86_64-linux-gnu/libmpi.so.40(ompi_mpi_init+0x252)[0x7f94ae62]
[myhost:39226] [11] 
/usr/lib/x86_64-linux-gnu/libmpi.so.40(PMPI_Init_thread+0x55)[0x7f94abbea2d5]
[myhost:39226] [12] 
/opt/gromacs-2018.6/bin/mdrun_mpi(+0x41e585)[0x55efb99a9585]
[myhost:39226] [13] 
/opt/gromacs-2018.6/bin/mdrun_mpi(+0x3da4d9)[0x55efb99654d9]
[myhost:39226] [14] 
/opt/gromacs-2018.6/bin/mdrun_mpi(+0xff6f9)[0x55efb968a6f9]
[myhost:39226] [15] 
/opt/gromacs-2018.6/bin/mdrun_mpi(+0xff919)[0x55efb968a919]
[myhost:39226] [16] 
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb)[0x7f94ab7e209b]
[myhost:39226] [17] 
/opt/gromacs-2018.6/bin/mdrun_mpi(+0xd4b7a)[0x55efb965fb7a]

[myhost:39226] *** End of error message ***


--
Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47| mailto:ta...@hegelab.org
Budapest, 1094, Hungary   | http://www.hegelab.org

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[gmx-users] replica exchange with GROMACS

[hind ahmed]

Hello
Could you please direct me to how  can I run job of  replica exchange  with 
GROMACS.  I used the setting bellow to submit the job on HEC, the job works but 
with no replex exchange and i got the note below.
#run the md
Mpirun -np 16 mdrun_mpi_d -multidir rep_0 rep_1 rep_2  rep_3  rep_4  rep_5  
rep_6  rep_7  rep_8  rep_9  rep_10 rep_11 rep_12 rep_13  rep_14 rep_15 -replex 
100
Is there any guide to how i run it right?

NOTE: The number of threads is not equal to the number of (logical) cores

  and the -pin option is set to auto: will not pin thread to cores.
  This can lead to significant performance degradation.
  Consider using -pin on (and -pinoffset in case you run multiple jobs).


Tthanks
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[gmx-users] How to prepare prm and itp files of ligands from gro and top files prepared with Gauss, ambertool and acpye for gromacs simulations

[Sun Yeping]

Dear everyone,

In order to perform gromacs simulations with ligand-protein complex, I have
to prepare the force field files for the ligand.
I first use Gauss to generate a Lig.gesp file which describe the
electrostatic potential. Then I use antechamber  from ambertool to fit the
gesp charges and generate a lig.mol2 file.

  antechamber -i Lig.gesp -fi gesp -o Lig.mol2 -fo mol2 -pf y -c resp

After that, I use parmchk2 to generate the frcmod file

  parmchk2 -i Lig.mol2 -f mol2 -o Lig.frcmod

Then the Lig.inpcrd coordinate file is prepared by tleap program from
ambertool, following which I use the acpye the generate the top and gro
files.

 acpype -p Lig.prmtop -x Lig.inpcrd -d

Now I have Lig.gro and Lig.top files in hand. However, to perform gromacs
simulation, I need the .prm and .itp files. Could you tell me how to get
these files?

Best regards.
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[gmx-users] Some out of date GROMPP warnings

[Joshua Mitchell]

Hi all,

I've noticed a couple of warnings from GROMPP that I think might be out of
date.

   1. When attempting to energy minimize with L-BFGS, VDW cutoffs and the
   force-switch modifier, GROMPP warns that "For efficient BFGS minimization,
   use switch/shift/pme instead of cut-off." However, switch and shift are
   deprecated. It's not clear to me whether this actually a relevant warning
   or if it just hasn't been updated since the new options were added and the
   old ones deprecated.
   2. Very small boxes (alanine dipeptide or pure water type stuff for
   benchmarking) with standard force fields often give me the error "The
   cut-off length is longer than half the shortest box vector or longer than
   the smallest box diagonal element. Increase the box size or decrease
   rlist." Since the group scheme is deprecated, and the Verlet scheme by
   default sets rlist automatically, this is a very confusing error.

Thanks! I love GROMACS very much.

 - Josh
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