Re: [gmx-users] Regarding the charge of the atom in the .rtp file

[Dilip H N]

Thank you for reply..

But how can i identify the molecule as methylamine (for example) since in
the .rtp the molecule type is written as [MAM1]
[ MAM1 ]
  [ atoms ]
   N1 NG321-0.990  0
   C1 CG3AM2 -0.060  1
  HN1 HGPAM20.390  2
  HN2 HGPAM20.390  3
  HC1 HGAAM20.090  4
  HC2 HGAAM20.090  5
  HC3 HGAAM20.090  6
  [ bonds ]
   N1C1
   N1   HN1
   N1   HN2
   C1   HC1
   C1   HC2
   C1   HC3
Is thr any hint such tht i can identify the molecule type written in .rtp
file.??
Or should i manually find it out..??... but in case of Glycine the molecule
type is [GLY] which is easy to find
How can i solve this issue..??

Thank you...



   Sent with Mailtrack


On Wed, Jun 21, 2017 at 4:23 PM, Mark Abraham 
wrote:

> Hi,
>
> On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
> wrote:
>
> > Hello all.
> > 1] I want to knw how the charges are designated/assigned for the each
> atoms
> > in molecule in the .rtp file.  ie., as example for methylamine in CHARMM
> > FF:-
> >
> > [ MAM1 ]
> >   [ atoms ]
> >   N1 NG321-0.990  0
> >   C1 CG3AM2 -0.060  1
> >  HN1 HGPAM20.390  2
> >  HN2 HGPAM20.390  3
> >  HC1 HGAAM20.090  4
> >  HC2 HGAAM20.090  5
> >  HC3 HGAAM20.090  6
> >   [ bonds ]
> >   N1C1
> >   N1   HN1
> >   N1   HN2
> >   C1   HC1
> >   C1   HC2
> >   C1   HC3
> >  ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...
> >
>
> The parameterization methodology is unique to each force field, and perhaps
> to each tool that generates compatible topologies. You need to read that
> documentation and literature to understand how they were derived.
>
>
> > 2] and if i get the topology/itp file from the automated topology builder
> > as in SwissParam for CHARMM forcefield, how can i confirm that the
> charges
> > assigned are exact..??
> >
>
> You can see if they are correct in the sense of being a valid model of
> reality by running a simulation and observing whether you can get
> reasonable agreement with suitable e.g. experimental data.
>
> Mark
>
>
> > Any help/suggestion is most welcome.
> > Thank you...
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student
> >
> >
> >
> >    Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature=en;
> referral=cy16f01.di...@nitk.edu.in=22
> > >
> > --
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-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] GROMACS and SIMtoEXP

[Sanim Rahman]

Thank you David,

I realized my mistake and I need to be using number density when working
with SIMtoEXP however, I was wondering if there is some script out there to
easily convert my number density from gromacs to the compatible file format
for SIMtoEXP.

Regards,
Sanim Rahman

On Wed, Jun 21, 2017 at 2:02 AM, David van der Spoel 
wrote:

> On 20/06/17 23:16, Sanim Rahman wrote:
>
>> Hello Everyone,
>>
>> I am interested in using the SIMtoEXP program to directly compare my
>> simulation results to experimental values. The program only can process
>> electron density profiles written as .dat and .sim files.
>>
>> Is anyone aware of scripts or GROMACS options that will allow me to output
>> my electron density profile into a .dat or .sim file that can be processed
>> by SIMtoEXP?
>>
>> Regards,
>> Sanim Rahman
>>
>> You have the wrong program if you need electron densities.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
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Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Jose Borreguero]

Victory! The -noparam did the trick :)
Thanks a million.

On Wed, Jun 21, 2017 at 11:43 AM, Justin Lemkul  wrote:

>
>
> On 6/21/17 11:39 AM, Jose Borreguero wrote:
>
>> Hi Justin,
>>
>> ​Thanks for your quick reply! ​
>> This means x2top is not finding
>> ​
>> or using
>> the right force constant value, right?
>> ​ I
>>
>> ​
>> did
>>   add the bond info into file ffbonded.itp
>> ​of
>> the oplsa.ff/ directory
>> ​
>> (https://goo.gl/z5UMot)
>> .
>> I also included the types in file
>> atomtypes.atp
>> ​
>>   and the non bonded info in
>> ffnonbonded.itp file. Maybe related to this issue is this line also found
>> in the output .top file:
>> ​​
>> #include "
>> ​​
>> ./oplsaa.ff/forcefield.itp"
>> This line should not be necessary because the .top​ file contains all
>> information. Does the line mean that the bond information in the output
>> .top file is overridden with that gmx later finds under
>> ​
>> ./oplsaa.ff
>> ​?
>> ​ If so, then the particular value of the force constant in the .top file
>> would  be irrelevant and my problem would be solved! :)
>>
>>
> Any value found in the .top overrides the force field.  Any blank in the
> topology is referenced from ffbonded.itp.  Anything missing after that
> generates a fatal error in grompp.  Use -noparam when running x2top if
> everything is accounted for in the force field parameter files.
>
>
> -Justin
>
> --
> ==
>
> 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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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 4:32 PM Shivangi Agarwal <
shivangi.agarwal...@gmail.com> wrote:

> Hi
> But it is broken. ..
>

Nope, it's just in one of the infinite number of equivalent representations
of the same thing ;-) mdrun doesn't know that you want it to write a file
where your protein and ligand and whatever strand are a cluster of things
that you'd like it to render centered in the same periodic cell. That's
what e.g. gmx trjconv -pbc cluster is useful for.

strand with proline with three odr residues has been broken and visible...
> i have Checked in vmd and pymol
>

Doesn't matter until you've said to a program "keep these things together"
:-)

Mark


> On 21 Jun 2017 17:16, "Mark Abraham"  wrote:
>
> > Hi,
> >
> > On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal <
> > shivangi.agarwal...@gmail.com> wrote:
> >
> > > Hello to all gmx users
> > >
> > > I am performing protein ligand complex MD simulation but my protein
> > > structure has been broken during energy minimization process.
> > >
> >
> > It's not broken, but rather in an unexpected representation. See
> > http://www.gromacs.org/Documentation/Terminology/
> > Periodic_Boundary_Conditions
> > for
> > background and suggestions.
> >
> > Mark
> >
> >
> > > What may be the suitable reason? How I can solve this?
> > > Your support is highly appreciated
> > > --
> > > 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] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda <
amanda.die...@imperial.ac.uk> wrote:

> Hi Justin,
> Thank you for your reply.
>
> Here are the links to the images of:
> -the output coordinates
> -and last frame of trajectory.
>
> Output coordinates which look wrong:
> http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_zp
> stuqkgjd2.png
> 
>
> Last frame from trajectory which looks OK:
> http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zpsn2
> 7nzusn.png
> 
>
> For the last frame of the trajectory I used trjconv -pbc nojump to make
> sure the atoms were not being wrapped around the box.


That's what you're getting. See "gmx help trjconv" where it specifically
says that "-pbc nojump" will lead to atoms appearing to diffuse out of the
box.

It seems like you want trjconv -pbc atom, so all the atoms are in the same
box. That won't necessarily match what mdrun -c writes, either, because
that is not something for which we have designed. There's an infinite
number of equivalent representations of any system, and a large number of
plausible representations that someone might want to use for different
purposes, so we've left the choice to you, with the tools and documentation
to get something that makes you happy :-)

Mark
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Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Diez Fernandez, Amanda]

Hi Justin, 
Thank you for your reply.

Here are the links to the images of:
-the output coordinates
-and last frame of trajectory.

Output coordinates which look wrong:
http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_zp
stuqkgjd2.png

Last frame from trajectory which looks OK:
http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zpsn2
7nzusn.png

For the last frame of the trajectory I used trjconv -pbc nojump to make
sure the atoms were not being wrapped around the box.
I am simulating an infinite silica slab, using a 4nm by 4nm unit cell.

Thanks!
Amanda


On 21/06/2017, 15:46, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-requ...@maillist.sys.kth.se"
 wrote:

>Send gromacs.org_gmx-users mailing list submissions to
>   gromacs.org_gmx-users@maillist.sys.kth.se
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>To subscribe or unsubscribe via the World Wide Web, visit
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>or, via email, send a message with subject or body 'help' to
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>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
>Today's Topics:
>
>   1. Re: (no subject) (Shivangi Agarwal)
>   2. Genion (Sergio Manzetti)
>   3. Re: non-bonded sigma for amino nitrogen?carboxylate oxygen
>  interactions in OPLSAA in GROMACS (gozde ergin)
>   4. Re: Difference between output_coordinates.gro and
>  trajectory.xtc coordinates (Justin Lemkul)
>   5. Re: Genion (Justin Lemkul)
>   6. Re: non-bonded sigma for amino nitrogen?carboxylate oxygen
>  interactions in OPLSAA in GROMACS (Justin Lemkul)
>
>
>--
>
>Message: 1
>Date: Wed, 21 Jun 2017 20:02:01 +0530
>From: Shivangi Agarwal 
>To: gmx-us...@gromacs.org
>Subject: Re: [gmx-users] (no subject)
>Message-ID:
>   
>Content-Type: text/plain; charset="UTF-8"
>
>Hi
>But it is broken. ..
>strand with proline with three odr residues has been broken and visible...
>i have Checked in vmd and pymol
>On 21 Jun 2017 17:16, "Mark Abraham"  wrote:
>
>> Hi,
>>
>> On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal <
>> shivangi.agarwal...@gmail.com> wrote:
>>
>> > Hello to all gmx users
>> >
>> > I am performing protein ligand complex MD simulation but my protein
>> > structure has been broken during energy minimization process.
>> >
>>
>> It's not broken, but rather in an unexpected representation. See
>> http://www.gromacs.org/Documentation/Terminology/
>> Periodic_Boundary_Conditions
>> for
>> background and suggestions.
>>
>> Mark
>>
>>
>> > What may be the suitable reason? How I can solve this?
>> > Your support is highly appreciated
>> > --
>> > 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/
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>>
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>>
>
>
>--
>
>Message: 2
>Date: Wed, 21 Jun 2017 16:30:01 +0200 (CEST)
>From: Sergio Manzetti 
>To: gmx-users 
>Subject: [gmx-users] Genion
>Message-ID:
>   <1713198892.5603815.1498055401007.javamail.zim...@fjordforsk.no>
>Content-Type: text/plain; charset=utf-8
>
>Hello, genion worked, and grompp was used to run the output conf from
>genion. Mdrun minimized all OK, however, mdrun produced a counfout.gro
>file that no longer contains the Na Cl ions added to the system. When
>setting up the simulation, the input confout.gro has no Na Cl ions, and
>the procedure is therefore not working.
>
>Why is this so? Does one have to do the genion procedure each time one
>wants to use gromp with a new mdp file?
>
>Sergio Manzetti 
>
>[ http://www.fjordforsk.no/logo_hr2.jpg ]
>
>[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/
>|   ] 
>Midtun 
>6894 Vangsnes 
>Norge 
>Org.nr. 911 659 654
>Tlf: +47 57695621 
>[ http://www.oekolab.com/ | ?kolab? ] | [ 

Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Justin Lemkul]

On 6/21/17 11:39 AM, Jose Borreguero wrote:

Hi Justin,

​Thanks for your quick reply! ​
This means x2top is not finding
​
or using
the right force constant value, right?
​ I

​
did
  add the bond info into file ffbonded.itp
​of
the oplsa.ff/ directory
​
(https://goo.gl/z5UMot)
.
I also included the types in file
atomtypes.atp
​
  and the non bonded info in
ffnonbonded.itp file. Maybe related to this issue is this line also found
in the output .top file:
​​
#include "
​​
./oplsaa.ff/forcefield.itp"
This line should not be necessary because the .top​ file contains all
information. Does the line mean that the bond information in the output
.top file is overridden with that gmx later finds under
​
./oplsaa.ff
​?
​ If so, then the particular value of the force constant in the .top file
would  be irrelevant and my problem would be solved! :)



Any value found in the .top overrides the force field.  Any blank in the 
topology is referenced from ffbonded.itp.  Anything missing after that generates 
a fatal error in grompp.  Use -noparam when running x2top if everything is 
accounted for in the force field parameter files.


-Justin

--
==

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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Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Jose Borreguero]

Hi Justin,

​Thanks for your quick reply! ​
This means x2top is not finding
​
or using
the right force constant value, right?
​ I

​
did
 add the bond info into file ffbonded.itp
​of
the oplsa.ff/ directory
​
(https://goo.gl/z5UMot)
.
I also included the types in file
atomtypes.atp
​
 and the non bonded info in
ffnonbonded.itp file. Maybe related to this issue is this line also found
in the output .top file:
​​
#include "
​​
./oplsaa.ff/forcefield.itp"
This line should not be necessary because the .top​ file contains all
information. Does the line mean that the bond information in the output
.top file is overridden with that gmx later finds under
​
./oplsaa.ff
​?
​ If so, then the particular value of the force constant in the .top file
would  be irrelevant and my problem would be solved! :)

​.Jose​

​


​.Jose​



On Wed, Jun 21, 2017 at 10:51 AM, Justin Lemkul  wrote:

>
>
> On 6/21/17 10:47 AM, Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> I created the .top file for a small silica crystal that contains only two
>> types of atoms, silicon (type SIO) and oxygen (type OSI). The bond
>> potential is:
>> [ bondtypes ]
>> ; ij  func   b0  kb
>>SIO OSI   1
>> ​ ​
>> 0.15783
>> ​   ​
>>251040
>>
>> After running gmx x2top, the .top file contains
>> [ bonds ]
>> ;  aiaj funct c0c1c2c3
>>  1 9 1  1.60e-01 4.00e+05  1.60e-01  4.00e+05
>>  135 1  1.60e-01 4.00e+05  1.60e-01  4.00e+05
>>
>> I
>> ​assume 0.16 in c0 and c2 is the result of rounding 0.15783, but I ​
>> was expecting number 251040 for c1 and c3, got
>> ​​
>> 40 instead
>> ​!
>> I don't know the meaning of coefficients c0, c1, c2, and c3
>> ​,​
>> I could not find some explanation for them
>> ​.
>> Can anyone point to a place where these coefficients are described in
>> detail? The description may explain the
>> ​
>> 40
>> ​ number.
>> ​
>>
>
> It's the default bonded force constant.
>
> gmx help x2top
> "
> ...
>  -kb   (40)   Bonded force constant (kJ/mol/nm^2)
> ...
> "
>
> The comment line means little, so there's no specific meaning to c0, c1,
> etc. It generically refers to bonded parameter fields, which for bonds are
> A- and B-state equilibrium lengths and force constants.  For dihedrals
> these mean something entirely different.
>
> -Justin
>
> --
> ==
>
> 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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Re: [gmx-users] Genion

[Sergio Manzetti]

Indeed, thanks: I did it manually. 

Will try updating the top with genion, 

Sergio 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, June 21, 2017 4:53:59 PM 
Subject: Re: [gmx-users] Genion 

On 6/21/17 10:45 AM, Sergio Manzetti wrote: 
> Hi Justin, the sequence was: 
> 
> gmx editconf  
> 
> gmx solvate  
> 
> gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr 
> 
> gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA 
> -nname CL 
> 
> then: 
> 
> gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o 
> dna_solv_NaCl_EM 
> 
> gmx mdrun 
> 
> 
> This worked. 
> 
> Then for the sim: 
> 
> dna_solv_NaCl_EM.gro does not contain any ions. 
> 

You didn't pass topol_solvated.top to genion -p, so it did not update the 
number 
of ions. Your final call to grompp should have triggered an error because the 
contents of the system will not match, unless you did this manually. But again, 
it is *impossible* for mdrun to delete anything. So check the contents of your 
files carefully, even just in a text editor for coordinates and topology, to 
make sure you have what you think you have. 

-Justin 

-- 
== 

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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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Justin Lemkul]

On 6/21/17 10:55 AM, gozde ergin wrote:

However in the paper they have mentioned that they increased the sigma  for 
amino nitrogen–carboxylate oxygen interactions
by 0.13Angstrom   relative to the original value.
So I assume there should be original value?
However you mentioned that there is no pair-specific LJ interaction in OPLSAA.
Even if I add a [nonbond_params] what epsilon and sigma should I use? Because 
they talk about the increment in sigma and I do not know the original value.
Maybe I should connect them directly.



Yes, do that to make sure they're consistent with the publication, but 
combination rules are explained in the PDF manual (and presumably in the 
original literature for the force field!) so you can calculate these very 
easily.  It's simple arithmetic.


-Justin

--
==

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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Re: [gmx-users] Genion

[Sergio Manzetti]

Hi Justin, the sequence was: 

gmx editconf  

gmx solvate  

gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr 

gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA 
-nname CL 

then: 

gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM 

gmx mdrun 


This worked. 

Then for the sim: 

dna_solv_NaCl_EM.gro does not contain any ions. 



Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Justin Lemkul"  
To: "gmx-users"  
Sent: Wednesday, June 21, 2017 4:44:16 PM 
Subject: Re: [gmx-users] Genion 

On 6/21/17 10:30 AM, Sergio Manzetti wrote: 
> Hello, genion worked, and grompp was used to run the output conf from genion. 
> Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no 
> longer contains the Na Cl ions added to the system. When setting up the 
> simulation, the input confout.gro has no Na Cl ions, and the procedure is 
> therefore not working. 
> 
> Why is this so? Does one have to do the genion procedure each time one wants 
> to use gromp with a new mdp file? 
> 

You run genion once to add ions to your system. Please provide the exact 
sequence of commands you're using. It's very hard to follow what you're 
describing. mdrun cannot delete anything, so "no longer contains the Na Cl 
ions" is impossible. Either the ions are there in the beginning or they're not. 
If you're using mdrun to run the .tpr file you're sending to genion, don't. 
There's no point. That .tpr file is not for a simulation, it's just for genion. 

-Justin 

-- 
== 

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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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

However in the paper they have mentioned that they increased the sigma  for 
amino nitrogen–carboxylate oxygen interactions 
by 0.13Angstrom   relative to the original value.
So I assume there should be original value? 
However you mentioned that there is no pair-specific LJ interaction in OPLSAA. 
Even if I add a [nonbond_params] what epsilon and sigma should I use? Because 
they talk about the increment in sigma and I do not know the original value.
Maybe I should connect them directly.

Thanks Justin.

> On 21 Jun 2017, at 16:46, Justin Lemkul  wrote:
> 
> 
> 
> On 6/21/17 10:39 AM, gozde ergin wrote:
>> Hi MArk,
>> Thanks for the respond. I understood that point however I still do not get 
>> which sigma to change.
>> I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
>> the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino 
>> notrogen and one for carboxylate oxygen.
>>  
>>  sigmaepsilon
>>  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
>>  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01
>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>> Which sigma should I change?
> 
> What people are doing more and more is introducing pair-specific parameters 
> to override the combination rule values.  That's likely what is being 
> referred to. OPLS-AA by default does not use pair-specific LJ interactions, 
> hence why you find no [nonbond_params] in ffnonbonded.itp.  The same is true 
> of AMBER.  CHARMM uses some (also called NBFIX in the literature), while 
> GROMOS uses a ton of these.
> 
> To override the LJ combination rules, add a [nonbond_params] directive with 
> the published parameters, which refer to an *interaction*, not an atom type.
> 
> -Justin
> 
>> Thanks
>>> On 21 Jun 2017, at 16:21, Mark Abraham  wrote:
>>> 
>>> Hi,
>>> 
>>> Different force fields work differently and thus are implemented
>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
>>> is a property of the atomtype
>>> 
>>> Mark
>>> 
>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:
>>> 
 Dear users,
 
 I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
 interactions in OPLSAA in GROMACS.
 However I have difficulties to understand which parameter i should change
 in ffnonbonded.itp file?
 I am looking something like [ nonbond_params ] section however it is not
 exist in ffnonbonded.itp?
 Any help would be appreciated.
 
 Thanks in advance.
 --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
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 * For (un)subscribe requests visit
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> 
> -- 
> ==
> 
> 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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Re: [gmx-users] Genion

[Justin Lemkul]

On 6/21/17 10:45 AM, Sergio Manzetti wrote:

Hi Justin, the sequence was:

gmx editconf 

gmx solvate 

gmx grompp -f em -c dna_solvated.gro -p topol_solvated -o dna_solv.tpr

gmx genion -s dna_solv.tpr -o dna_solv_NaCl.gro -conc 0.15 -neutral -pname NA 
-nname CL

then:

gmx grompp -f em.mdp -c dna_solv_NaCl.gro -p topol_solvated -o dna_solv_NaCl_EM

gmx mdrun


This worked.

Then for the sim:

dna_solv_NaCl_EM.gro does not contain any ions.



You didn't pass topol_solvated.top to genion -p, so it did not update the number 
of ions.  Your final call to grompp should have triggered an error because the 
contents of the system will not match, unless you did this manually.  But again, 
it is *impossible* for mdrun to delete anything.  So check the contents of your 
files carefully, even just in a text editor for coordinates and topology, to 
make sure you have what you think you have.


-Justin

--
==

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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Re: [gmx-users] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Justin Lemkul]

On 6/21/17 10:47 AM, Jose Borreguero wrote:

Dear Gromacs users,

I created the .top file for a small silica crystal that contains only two
types of atoms, silicon (type SIO) and oxygen (type OSI). The bond
potential is:
[ bondtypes ]
; ij  func   b0  kb
   SIO OSI   1
​ ​
0.15783
​   ​
   251040

After running gmx x2top, the .top file contains
[ bonds ]
;  aiaj funct c0c1c2c3
 1 9 1  1.60e-01 4.00e+05  1.60e-01  4.00e+05
 135 1  1.60e-01 4.00e+05  1.60e-01  4.00e+05

I
​assume 0.16 in c0 and c2 is the result of rounding 0.15783, but I ​
was expecting number 251040 for c1 and c3, got
​​
40 instead
​!
I don't know the meaning of coefficients c0, c1, c2, and c3
​,​
I could not find some explanation for them
​.
Can anyone point to a place where these coefficients are described in
detail? The description may explain the
​
40
​ number.
​


It's the default bonded force constant.

gmx help x2top
"
...
 -kb   (40)   Bonded force constant (kJ/mol/nm^2)
...
"

The comment line means little, so there's no specific meaning to c0, c1, etc. 
It generically refers to bonded parameter fields, which for bonds are A- and 
B-state equilibrium lengths and force constants.  For dihedrals these mean 
something entirely different.


-Justin

--
==

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] puzzled by unexpected [ bonds ] section resulting from running gmx x2top

[Jose Borreguero]

Dear Gromacs users,

I created the .top file for a small silica crystal that contains only two
types of atoms, silicon (type SIO) and oxygen (type OSI). The bond
potential is:
[ bondtypes ]
; ij  func   b0  kb
  SIO OSI   1
​ ​
   0.15783
​   ​
  251040

After running gmx x2top, the .top file contains
[ bonds ]
;  aiaj funct c0c1c2c3
1 9 1  1.60e-01 4.00e+05  1.60e-01  4.00e+05
135 1  1.60e-01 4.00e+05  1.60e-01  4.00e+05

I
​assume 0.16 in c0 and c2 is the result of rounding 0.15783, but I ​
was expecting number 251040 for c1 and c3, got
​​
40 instead
​!
I don't know the meaning of coefficients c0, c1, c2, and c3
​,​
I could not find some explanation for them
​.
Can anyone point to a place where these coefficients are described in
detail? The description may explain the
​
40
​ number.
​

Best,
.Jose
​
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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Justin Lemkul]

On 6/21/17 10:39 AM, gozde ergin wrote:

Hi MArk,

Thanks for the respond. I understood that point however I still do not get 
which sigma to change.
I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
the for nitrogen–carboxylate oxygen interactions in OPLSAA.
However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino notrogen 
and one for carboxylate oxygen.

   
sigmaepsilon
  opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
  opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01

Which one defines the amino nitrogen–carboxylate oxygen interactions?
Which sigma should I change?



What people are doing more and more is introducing pair-specific parameters to 
override the combination rule values.  That's likely what is being referred to. 
OPLS-AA by default does not use pair-specific LJ interactions, hence why you 
find no [nonbond_params] in ffnonbonded.itp.  The same is true of AMBER.  CHARMM 
uses some (also called NBFIX in the literature), while GROMOS uses a ton of these.


To override the LJ combination rules, add a [nonbond_params] directive with the 
published parameters, which refer to an *interaction*, not an atom type.


-Justin


Thanks

On 21 Jun 2017, at 16:21, Mark Abraham  wrote:

Hi,

Different force fields work differently and thus are implemented
differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
is a property of the atomtype

Mark

On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:


Dear users,

I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
interactions in OPLSAA in GROMACS.
However I have difficulties to understand which parameter i should change
in ffnonbonded.itp file?
I am looking something like [ nonbond_params ] section however it is not
exist in ffnonbonded.itp?
Any help would be appreciated.

Thanks in advance.
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--
==

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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Re: [gmx-users] Genion

[Justin Lemkul]

On 6/21/17 10:30 AM, Sergio Manzetti wrote:

Hello, genion worked, and grompp was used to run the output conf from genion. 
Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no 
longer contains the Na Cl ions added to the system. When setting up the 
simulation, the input confout.gro has no Na Cl ions, and the procedure is 
therefore not working.

Why is this so? Does one have to do the genion procedure each time one wants to 
use gromp with a new mdp file?



You run genion once to add ions to your system.  Please provide the exact 
sequence of commands you're using.  It's very hard to follow what you're 
describing.  mdrun cannot delete anything, so "no longer contains the Na Cl 
ions" is impossible.  Either the ions are there in the beginning or they're not. 
 If you're using mdrun to run the .tpr file you're sending to genion, don't. 
There's no point.  That .tpr file is not for a simulation, it's just for genion.


-Justin

--
==

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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Re: [gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Justin Lemkul]

On 6/21/17 7:11 AM, Diez Fernandez, Amanda wrote:

Hi all,
I am running a simulation and I find that the output coordinates of the 
simulation stored in “final_coordinates.gro” are distinctively different to any 
of the frames from “trajectory.gro” which I obtain from :

trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro

When I visualise final_coordinates.gro they look wrong, when I visualise 
trajectory.gro frame by frame it looks correct.

How can this be possible? Is it a common problem?



Please define what "wrong" and "correct" mean.  The raw trajectory from mdrun 
does not have PBC-corrected frames, so things may be broken.  If you're done 
reimaging with trjconv, you've changed the representation.  You can dump the 
final coordinates from the .xtc, make molecules whole, and these should match 
the final configuration written by mdrun.


-Justin

--
==

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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Re: [gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Hi MArk,

Thanks for the respond. I understood that point however I still do not get 
which sigma to change.
I the paper JCTC 2017, Miller et. al. they have mentioned that they increase 
the for nitrogen–carboxylate oxygen interactions in OPLSAA.
However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino notrogen 
and one for carboxylate oxygen.

  
sigmaepsilon
 opls_287   N3   7  14.00670-0.300   A3.25000e-01  7.11280e-01
 opls_272   O2   8  15.99940-0.800   A2.96000e-01  8.78640e-01

Which one defines the amino nitrogen–carboxylate oxygen interactions?
Which sigma should I change?

Thanks
> On 21 Jun 2017, at 16:21, Mark Abraham  wrote:
> 
> Hi,
> 
> Different force fields work differently and thus are implemented
> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
> is a property of the atomtype
> 
> Mark
> 
> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:
> 
>> Dear users,
>> 
>> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
>> interactions in OPLSAA in GROMACS.
>> However I have difficulties to understand which parameter i should change
>> in ffnonbonded.itp file?
>> I am looking something like [ nonbond_params ] section however it is not
>> exist in ffnonbonded.itp?
>> Any help would be appreciated.
>> 
>> Thanks in advance.
>> --
>> Gromacs Users mailing list
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[gmx-users] Genion

[Sergio Manzetti]

Hello, genion worked, and grompp was used to run the output conf from genion. 
Mdrun minimized all OK, however, mdrun produced a counfout.gro file that no 
longer contains the Na Cl ions added to the system. When setting up the 
simulation, the input confout.gro has no Na Cl ions, and the procedure is 
therefore not working. 

Why is this so? Does one have to do the genion procedure each time one wants to 
use gromp with a new mdp file? 

Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 

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Re: [gmx-users] (no subject)

[Shivangi Agarwal]

Hi
But it is broken. ..
strand with proline with three odr residues has been broken and visible...
i have Checked in vmd and pymol
On 21 Jun 2017 17:16, "Mark Abraham"  wrote:

> Hi,
>
> On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal <
> shivangi.agarwal...@gmail.com> wrote:
>
> > Hello to all gmx users
> >
> > I am performing protein ligand complex MD simulation but my protein
> > structure has been broken during energy minimization process.
> >
>
> It's not broken, but rather in an unexpected representation. See
> http://www.gromacs.org/Documentation/Terminology/
> Periodic_Boundary_Conditions
> for
> background and suggestions.
>
> Mark
>
>
> > What may be the suitable reason? How I can solve this?
> > Your support is highly appreciated
> > --
> > 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] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[Mark Abraham]

Hi,

Different force fields work differently and thus are implemented
differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
is a property of the atomtype

Mark

On Wed, Jun 21, 2017 at 4:16 PM gozde ergin  wrote:

> Dear users,
>
> I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
> interactions in OPLSAA in GROMACS.
> However I have difficulties to understand which parameter i should change
> in ffnonbonded.itp file?
> I am looking something like [ nonbond_params ] section however it is not
> exist in ffnonbonded.itp?
> Any help would be appreciated.
>
> Thanks in advance.
> --
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[gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

[gozde ergin]

Dear users,

I am trying to change the sigma value of amino nitrogen–carboxylate oxygen 
interactions in OPLSAA in GROMACS.
However I have difficulties to understand which parameter i should change in 
ffnonbonded.itp file?
I am looking something like [ nonbond_params ] section however it is not exist 
in ffnonbonded.itp?
Any help would be appreciated.

Thanks in advance.
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Re: [gmx-users] Error running GMX 5.14

[Sergio Manzetti]

Thanks, this worked. 

Sergio 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ] 



From: "Mark Abraham"  
To: "gmx-users"  
Sent: Tuesday, June 20, 2017 5:04:24 PM 
Subject: Re: [gmx-users] Error running GMX 5.14 

Hi, 

# make initial gro and .top somehow 
gmx grompp -f whatever -c initial -p initial -o for-genion 
cp initial.top with-ions.top 
gmx genion -f for-genion -p with-ions.top -o with-ions 
gmx grompp -f em -p with-ions -c with-ions -o ready-for-em 
gmx mdrun -s ready-for-em 

Mark 

On Tue, Jun 20, 2017 at 4:45 PM Sergio Manzetti < 
sergio.manze...@fjordforsk.no> wrote: 

> Precisely. Thanks. 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 <+47%2057%2069%2056%2021> 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
> 
> 
> From: "Justin Lemkul"  
> To: "gmx-users"  
> Sent: Tuesday, June 20, 2017 4:42:37 PM 
> Subject: Re: [gmx-users] Error running GMX 5.14 
> 
> On 6/20/17 10:36 AM, Sergio Manzetti wrote: 
> > One simple question, where does one get the sytem input for genion, as 
> it only want tpr, unless one uses grompp? 
> > 
> 
> Yes, you have to use grompp on the solvated system to get a .tpr of the 
> system 
> that contains no ions. You pass that .tpr to genion and then never use it 
> again. 
> 
> -Justin 
> 
> > 
> > Sergio Manzetti 
> > 
> > [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> > 
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ 
> http://www.fjordforsk.no/ | ] 
> > Midtun 
> > 6894 Vangsnes 
> > Norge 
> > Org.nr. 911 659 654 
> > Tlf: +47 57695621 <+47%2057%2069%2056%2021> 
> > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ 
> | FAP ] 
> > 
> > 
> > 
> > From: "Justin Lemkul"  
> > To: "gmx-users"  
> > Sent: Tuesday, June 20, 2017 4:39:03 PM 
> > Subject: Re: [gmx-users] Error running GMX 5.14 
> > 
> > On 6/20/17 10:32 AM, Sergio Manzetti wrote: 
> >> Let me see if I have it right. 
> >> 
> >> After doing the minimization of the system without ions, I add ions to 
> the minimized system and replace the waters. 
> >> 
> > 
> > I see no point in doing multiple rounds of minimization like this. Just 
> build 
> > the whole system and minimize. 
> > 
> >> Then I use grompp to set up the sim with the output tpr from the genion 
> command as -c file, and the original topology ? 
> >> 
> > 
> > No. The .tpr file provided to genion is never used again. It has one 
> purpose 
> > only and it is not an output from genion at all. 
> > 
> > This is all very basic stuff. Please try some tutorials: 
> > 
> > http://www.gromacs.org/Documentation/Tutorials#General_GROMACS_Use 
> > 
> > -Justin 
> > 
> >> Sergio 
> >> 
> >> 
> >> Sergio Manzetti 
> >> 
> >> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> >> 
> >> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ 
> http://www.fjordforsk.no/ | ] 
> >> Midtun 
> >> 6894 Vangsnes 
> >> Norge 
> >> Org.nr. 911 659 654 
> >> Tlf: +47 57695621 <+47%2057%2069%2056%2021> 
> >> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ 
> | FAP ] 
> >> 
> >> 
> >> 
> >> From: "Justin Lemkul"  
> >> To: "gmx-users"  
> >> Sent: Tuesday, June 20, 2017 4:21:18 PM 
> >> Subject: Re: [gmx-users] Error running GMX 5.14 
> >> 
> >> On 6/20/17 10:14 AM, Sergio Manzetti wrote: 
> >>> I run the simulations on the solvated DNA without adding ions. Then at 
> the end, I added ions to the output tpr of the simulation. At this stage I 
> waanted then to run the simulaiton with the new tpr. But that does not work. 
> >>> 
> >> 
> >> How did you add ions to a .tpr? This implies adding them to a 
> coordinate file, 
> >> then adding them to the topology, and correctly compiling a .tpr with 
> grompp. 
> >> Depending on how you did this, it's likely the cause of your problem. 
> >> 
> >>> Is there a tutorial online on how to add Na to DNA with command line? 
> >>> 
> >> 
> >> It's no different than any invocation of genion, which you can get from 
> any 
> >> tutorial. For instance: 
> >> 
> >> gmx genion -s dna_solv.tpr -o dna_solv_ions.gro -p topol.top -pname NA 
> -np 20 
> >> 
> >> -Justin 
> >> 
> > 
> 

Re: [gmx-users] Slow MDRUN performance

[Mark Abraham]

Hi,

OK. The build system will choose these defaults correctly for you if you
just leave things alone ;-)

Mark

On Wed, Jun 21, 2017 at 1:17 PM Syed Azeem 
wrote:

> >
> > Hi,
> >
> > On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem  >
> > wrote:
> >
> >> Hi all,
> >>
> >> I installed gromacs 5.1.2 on a new machine.
> >> Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.
> >>
> >> Then I started a NVT simulation for 500ps with ~25 atom system.
> >> Surprisingly, the estimated time was 4 days and 3 hours.
> >>
> >> There was a note stating consider rebuilding gmx with the
> >> GMX_USE_RDTSCP=ON CMake option, as follows:
> >>
> >> GROMACS:  gmx mdrun, VERSION 5.1.2
> >> Executable:   /usr/local/gromacs/bin/gmx
> >> Data prefix:  /usr/local/gromacs
> >> Command line:
> >>   gmx mdrun -v -deffnm nvt
> >>
> >>
> >> Running on 1 node with total 4 cores, 4 logical cores
> >> Hardware detected:
> >>   CPU info:
> >> Vendor: GenuineIntel
> >> Brand:  Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
> >> SIMD instructions most likely to fit this hardware: AVX2_256
> >> SIMD instructions selected at GROMACS compile time: None
> >>
> >> Compiled SIMD instructions: None, GROMACS could use AVX2_256 on this
> >> machine, which is better
> >>
> >>
> >> The current CPU can measure timings more accurately than the code in
> >> gmx was configured to use. This might affect your simulation
> >> speed as accurate timings are needed for load-balancing.
> >> Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.
> >>
> >> Reading file em.tpr, VERSION 5.1.2 (single precision)
> >> Using 1 MPI thread
> >> Using 4 OpenMP threads
> >>
> >>
> >> WARNING: Using the slow plain C kernels. This should
> >> not happen during routine usage on supported platforms.
> >>
> >> Then, I rebuilt gromacs with the CMAKE GMX_USE_RDTSCP=ON, as suggested.
> >>
> >> Again the performance is slow with the same note being generated.
> >>
> >> PS: For comparison, I ran 500 ps NVT simulation of the same ~25
> >> atom system on another machine of the same config and finished within
> >> 7 hours.
> >>
> >> What mistake am I making in the installation?
> >>
> >
> > We can't tell, because you didn't tell us about how the installation was
> > done. ;-) But somehow everything useful got turned off, so don't do that.
> > You should use the quick and dirty guide at
> > http://manual.gromacs.org/documentation/5.1.4/install-guide/index.html,
> > configure on the node you'll run on, and install the latest in the 5.1
> > series, not an older one with extra bugs ;-)
> >
> > Mark
> Thanks for the reply, Mark.
>
> I followed the quick and dirty installation from the gromacs
> installation documentation.
>
> Now I rectified the problem by rebuilding GMX with GMX_USE_RDTSCP=ON
> and -DGMX_SIMD=AVE2_256, which gromacs suggested would be better for
> my machine.
>
> Azeem
> >
> >
> >> Thanks in advance,
> >>
> >> Azeem
> >> --
> --
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 1:21 PM Shivangi Agarwal <
shivangi.agarwal...@gmail.com> wrote:

> Hello to all gmx users
>
> I am performing protein ligand complex MD simulation but my protein
> structure has been broken during energy minimization process.
>

It's not broken, but rather in an unexpected representation. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
for
background and suggestions.

Mark


> What may be the suitable reason? How I can solve this?
> Your support is highly appreciated
> --
> Gromacs Users mailing list
>
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[gmx-users] (no subject)

[Shivangi Agarwal]

Hello to all gmx users

I am performing protein ligand complex MD simulation but my protein
structure has been broken during energy minimization process.

What may be the suitable reason? How I can solve this?
Your support is highly appreciated
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Re: [gmx-users] Slow MDRUN performance

[Syed Azeem]

>
> Hi,
>
> On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem 
> wrote:
>
>> Hi all,
>>
>> I installed gromacs 5.1.2 on a new machine.
>> Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.
>>
>> Then I started a NVT simulation for 500ps with ~25 atom system.
>> Surprisingly, the estimated time was 4 days and 3 hours.
>>
>> There was a note stating consider rebuilding gmx with the
>> GMX_USE_RDTSCP=ON CMake option, as follows:
>>
>> GROMACS:  gmx mdrun, VERSION 5.1.2
>> Executable:   /usr/local/gromacs/bin/gmx
>> Data prefix:  /usr/local/gromacs
>> Command line:
>>   gmx mdrun -v -deffnm nvt
>>
>>
>> Running on 1 node with total 4 cores, 4 logical cores
>> Hardware detected:
>>   CPU info:
>> Vendor: GenuineIntel
>> Brand:  Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
>> SIMD instructions most likely to fit this hardware: AVX2_256
>> SIMD instructions selected at GROMACS compile time: None
>>
>> Compiled SIMD instructions: None, GROMACS could use AVX2_256 on this
>> machine, which is better
>>
>>
>> The current CPU can measure timings more accurately than the code in
>> gmx was configured to use. This might affect your simulation
>> speed as accurate timings are needed for load-balancing.
>> Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.
>>
>> Reading file em.tpr, VERSION 5.1.2 (single precision)
>> Using 1 MPI thread
>> Using 4 OpenMP threads
>>
>>
>> WARNING: Using the slow plain C kernels. This should
>> not happen during routine usage on supported platforms.
>>
>> Then, I rebuilt gromacs with the CMAKE GMX_USE_RDTSCP=ON, as suggested.
>>
>> Again the performance is slow with the same note being generated.
>>
>> PS: For comparison, I ran 500 ps NVT simulation of the same ~25
>> atom system on another machine of the same config and finished within
>> 7 hours.
>>
>> What mistake am I making in the installation?
>>
>
> We can't tell, because you didn't tell us about how the installation was
> done. ;-) But somehow everything useful got turned off, so don't do that.
> You should use the quick and dirty guide at
> http://manual.gromacs.org/documentation/5.1.4/install-guide/index.html,
> configure on the node you'll run on, and install the latest in the 5.1
> series, not an older one with extra bugs ;-)
>
> Mark
Thanks for the reply, Mark.

I followed the quick and dirty installation from the gromacs
installation documentation.

Now I rectified the problem by rebuilding GMX with GMX_USE_RDTSCP=ON
and -DGMX_SIMD=AVE2_256, which gromacs suggested would be better for
my machine.

Azeem
>
>
>> Thanks in advance,
>>
>> Azeem
>> --
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[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Diez Fernandez, Amanda]

Hi all,
I am running a simulation and I find that the output coordinates of the 
simulation stored in “final_coordinates.gro” are distinctively different to any 
of the frames from “trajectory.gro” which I obtain from :

trjconv –s file.tpr –f trajectory.xtc –o trajectory.gro

When I visualise final_coordinates.gro they look wrong, when I visualise 
trajectory.gro frame by frame it looks correct.

How can this be possible? Is it a common problem?

Thank you,

Amanda
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Re: [gmx-users] Protein-ligand binding Cut-offs

[Mark Abraham]

Hi,

You aren't getting output because you aren't actually making a selection -
see "gmx help select" and its suggestions for where to look for the rest of
the documentation and explained examples.

Mark

On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash 
wrote:

> I'm not sure if the command I entered (shown below) is correct. No output
> was given. I'm unclear as to how this command will enable me to isolate the
> glycine molecules within 4A of the protein molecule?
>
> gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos whole_mol_com
> -seltype dyn_mol_com -pdbatoms all
>
> Akash
>
> -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 Mark
> Abraham
> Sent: 16 June 2017 17:22
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> Hi,
>
> Gmx select will produce a selection eg of all molecules with an atom
> within a cutoff of any atom in another molecule.
>
> Mark
>
> On Fri, 16 Jun 2017 18:15 Pandya, Akash  wrote:
>
> > Hi all,
> >
> > I have ran a simulation with a protein and multiple ligand molecules
> > inserted randomly inside a box. I want to isolate those ligand
> > molecules that are closest to the protein by a cut-off of four
> > angstroms or so. Is there a command I could use to do this for me or
> > would I have to use a molecular visualizer software for this?
> >
> > Thanks,
> >
> > Akash
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Regarding the charge of the atom in the .rtp file

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 11:59 AM Dilip H N 
wrote:

> Hello all.
> 1] I want to knw how the charges are designated/assigned for the each atoms
> in molecule in the .rtp file.  ie., as example for methylamine in CHARMM
> FF:-
>
> [ MAM1 ]
>   [ atoms ]
>   N1 NG321-0.990  0
>   C1 CG3AM2 -0.060  1
>  HN1 HGPAM20.390  2
>  HN2 HGPAM20.390  3
>  HC1 HGAAM20.090  4
>  HC2 HGAAM20.090  5
>  HC3 HGAAM20.090  6
>   [ bonds ]
>   N1C1
>   N1   HN1
>   N1   HN2
>   C1   HC1
>   C1   HC2
>   C1   HC3
>  ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...
>

The parameterization methodology is unique to each force field, and perhaps
to each tool that generates compatible topologies. You need to read that
documentation and literature to understand how they were derived.


> 2] and if i get the topology/itp file from the automated topology builder
> as in SwissParam for CHARMM forcefield, how can i confirm that the charges
> assigned are exact..??
>

You can see if they are correct in the sense of being a valid model of
reality by running a simulation and observing whether you can get
reasonable agreement with suitable e.g. experimental data.

Mark


> Any help/suggestion is most welcome.
> Thank you...
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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Re: [gmx-users] Slow MDRUN performance

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 12:47 PM Syed Azeem 
wrote:

> Hi all,
>
> I installed gromacs 5.1.2 on a new machine.
> Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.
>
> Then I started a NVT simulation for 500ps with ~25 atom system.
> Surprisingly, the estimated time was 4 days and 3 hours.
>
> There was a note stating consider rebuilding gmx with the
> GMX_USE_RDTSCP=ON CMake option, as follows:
>
> GROMACS:  gmx mdrun, VERSION 5.1.2
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>   gmx mdrun -v -deffnm nvt
>
>
> Running on 1 node with total 4 cores, 4 logical cores
> Hardware detected:
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
> SIMD instructions most likely to fit this hardware: AVX2_256
> SIMD instructions selected at GROMACS compile time: None
>
> Compiled SIMD instructions: None, GROMACS could use AVX2_256 on this
> machine, which is better
>
>
> The current CPU can measure timings more accurately than the code in
> gmx was configured to use. This might affect your simulation
> speed as accurate timings are needed for load-balancing.
> Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.
>
> Reading file em.tpr, VERSION 5.1.2 (single precision)
> Using 1 MPI thread
> Using 4 OpenMP threads
>
>
> WARNING: Using the slow plain C kernels. This should
> not happen during routine usage on supported platforms.
>
> Then, I rebuilt gromacs with the CMAKE GMX_USE_RDTSCP=ON, as suggested.
>
> Again the performance is slow with the same note being generated.
>
> PS: For comparison, I ran 500 ps NVT simulation of the same ~25
> atom system on another machine of the same config and finished within
> 7 hours.
>
> What mistake am I making in the installation?
>

We can't tell, because you didn't tell us about how the installation was
done. ;-) But somehow everything useful got turned off, so don't do that.
You should use the quick and dirty guide at
http://manual.gromacs.org/documentation/5.1.4/install-guide/index.html,
configure on the node you'll run on, and install the latest in the 5.1
series, not an older one with extra bugs ;-)

Mark


> Thanks in advance,
>
> Azeem
> --
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[gmx-users] Slow MDRUN performance

[Syed Azeem]

Hi all,

I installed gromacs 5.1.2 on a new machine.
Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.

Then I started a NVT simulation for 500ps with ~25 atom system.
Surprisingly, the estimated time was 4 days and 3 hours.

There was a note stating consider rebuilding gmx with the
GMX_USE_RDTSCP=ON CMake option, as follows:

GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -v -deffnm nvt


Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: None

Compiled SIMD instructions: None, GROMACS could use AVX2_256 on this
machine, which is better


The current CPU can measure timings more accurately than the code in
gmx was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads


WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.

Then, I rebuilt gromacs with the CMAKE GMX_USE_RDTSCP=ON, as suggested.

Again the performance is slow with the same note being generated.

PS: For comparison, I ran 500 ps NVT simulation of the same ~25
atom system on another machine of the same config and finished within
7 hours.

What mistake am I making in the installation?

Thanks in advance,

Azeem
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Re: [gmx-users] Protein-ligand binding Cut-offs

[Pandya, Akash]

I'm not sure if the command I entered (shown below) is correct. No output was 
given. I'm unclear as to how this command will enable me to isolate the glycine 
molecules within 4A of the protein molecule?  

gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos whole_mol_com 
-seltype dyn_mol_com -pdbatoms all

Akash

-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 Mark 
Abraham
Sent: 16 June 2017 17:22
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

Hi,

Gmx select will produce a selection eg of all molecules with an atom within a 
cutoff of any atom in another molecule.

Mark

On Fri, 16 Jun 2017 18:15 Pandya, Akash  wrote:

> Hi all,
>
> I have ran a simulation with a protein and multiple ligand molecules 
> inserted randomly inside a box. I want to isolate those ligand 
> molecules that are closest to the protein by a cut-off of four 
> angstroms or so. Is there a command I could use to do this for me or 
> would I have to use a molecular visualizer software for this?
>
> Thanks,
>
> Akash
> --
> Gromacs Users mailing list
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before 
> posting!
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[gmx-users] Regarding the charge of the atom in the .rtp file

[Dilip H N]

Hello all.
1] I want to knw how the charges are designated/assigned for the each atoms
in molecule in the .rtp file.  ie., as example for methylamine in CHARMM
FF:-

[ MAM1 ]
  [ atoms ]
  N1 NG321-0.990  0
  C1 CG3AM2 -0.060  1
 HN1 HGPAM20.390  2
 HN2 HGPAM20.390  3
 HC1 HGAAM20.090  4
 HC2 HGAAM20.090  5
 HC3 HGAAM20.090  6
  [ bonds ]
  N1C1
  N1   HN1
  N1   HN2
  C1   HC1
  C1   HC2
  C1   HC3
 ie how are the charges -0.990, -0.060, 0.390 etc., are assigned...

2] and if i get the topology/itp file from the automated topology builder
as in SwissParam for CHARMM forcefield, how can i confirm that the charges
assigned are exact..??

Any help/suggestion is most welcome.
Thank you...
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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Re: [gmx-users] Computing work from pulling simulations

[Leandro Bortot]

Have you compared the results of your calculation using the forces at
different intervals? e.g. every 1, 10, 50, 100 steps ?

As long as you use a not-so-large interval the result should be the same
within statistical error.

Cheers,
Leandro


On Mon, Jun 19, 2017 at 7:19 PM, Lutz Maibaum 
wrote:

> I am using “umbrella pulling” to simulate the dissociation of two
> molecules. I would like to calculate the work W(t) that the harmonic trap
> has performed on my system up to timestep t, which can be calculated as
>
> W(t) = sum_{i=0}^t F_i * v * dt
>
> where F_i is the biasing force at timestep i, v is the pulling velocity,
> and dt is the timestep. The latter two I set in the .mdp file, and the
> force is written out by Gromacs to the  pull_pullf.xvg file.
>
> This works very well. However, computing the work using the equation above
> requires me to save the forces to a file _every single timestep_, which
> becomes unfeasible for longer simulations. Does Gromacs keep track of the
> cumulative work performed by the umbrella potential, and does it save that
> value somewhere? I couldn’t find it in the .edr or log files (I am using
> Gromacs 5.1.4).
>
> Best,
>
> Lutz
>
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Re: [gmx-users] a problem about ewald geometry=3dc

[Philip Loche]

If you can not make sure that the atoms stay inside the slab you should use 3D 
electrostatics. The 3DC method an approximation, which gives the same results 
as true 2D electrostatics only for a thin slab. When atoms leave the slab the 
potentials and forces comparing 2D and 3DC are not consistent anymore.

Best

Philip

> On 20. Jun 2017, at 18:25, Ali Shomali  wrote:
> 
> Dear Philip
> 
> Thanks for your helpful advice
> 
> Actually, my simulation case is a slab of water that is covered by
> monolayer in just one surface and the other surface is free and sometimes
> some of water molecules (small number) escape from it. So is 3dc option
> still applicable or I should return to original 3d method?
> I appreciate your valuable suggestions.
> Thanks
> 
> Ali
> 
> 
> On Tue, Jun 20, 2017 at 6:50 PM, Philip Loche 
> wrote:
> 
>> Dear Ali,
>> 
>> to use the 2D correction you only have to make sure that your box height
>> is at least 3 times larger than your slab. This does not depend on the
>> explicit position of your slab. So pbc=xyz does not make any problems, if
>> your atoms always “stay” in a thin slab and do not move around in the whole
>> box! The whole technique is explained in this paper:
>> http://dx.doi.org/10.1063/1.479595
>> 
>> Best
>> 
>> Philip
>> 
>> 
>> —
>> 
>> Philip Loche
>> Department of Physics
>> Freie Universität Berlin
>> Arnimallee 14, Room 0.3.30
>> 14195 Berlin, Germany
>> 
>> phone: +49 (0)30/838-55279
>> 
>>> On 19. Jun 2017, at 21:37, Ali Shomali  wrote:
>>> 
>>> Hello to all Dear Gromacs Users
>>> 
>>> I'm modeling a lipid monolayer with vacuum space on top of it and with
>>> periodic boundary conditions in xyz directions. the vacuum space is about
>>> 10nm to minimize any possible effect of periodicity. for using ewald
>>> summation as manual mentions :
>>> 
>>> *"The geometry to use for Ewald summations. 3d means the sum is performed
>>> in all three dimensions. If your system has a slab geometry in the x-y
>>> plane you can try to increase box z dimension and use the 3dc geometry.
>> The
>>> reciprocal sum is still performed in 3d, but a force and potential
>>> correction applied in the z dimension to produce a pseudo-2d summation.
>> In
>>> the future there might also be a true2d option, but this is not working
>> y"*
>>> 
>>> 
>>> however it causes warning :
>>> 
>>> With PME and ewald_geometry = 3dc you should use pbc = xy
>>> 
>>> since I can't use pbc=xy , can I use 3dc with pbc in xyz and ignore the
>>> warning ? how this affect results?
>>> 
>>> Thanks for your time and attention
>>> Ali
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>> send a mail to gmx-users-requ...@gromacs.org.
>> 
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Re: [gmx-users] Difference between Err. Est. And RMSD

[jay patil]

Thanks João for the answer.
Thanks Justin for sharing reference.

Justin,
What will be your brief suggestion for the question, " which one among Err.Est 
or RMSD should I use to show error bars in the plot. "
If I have to report box-X and  box-Y in the publication.

Thank you.

> On 20-Jun-2017, at 5:25 PM, Justin Lemkul  wrote:
> 
> 
> 
>> On 6/20/17 7:44 AM, jay patil wrote:
>> Hi all,
>> When we get averages from energy file using gmx energy -f *.edr
>> Output shows Average Err.Est RMSD Tot-Drift.
>> Which one among Err.Est or RMSD should I use to show error bars in the plot.
>> By definition I know RMSD, what is formula for Err.Est.
> 
> See the appendix of dx.doi.org/10.1063/1.1421362
> 
> -Justin
> 
> 
> -- 
> ==
> 
> 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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Re: [gmx-users] GROMACS and SIMtoEXP

[David van der Spoel]

On 20/06/17 23:16, Sanim Rahman wrote:

Hello Everyone,

I am interested in using the SIMtoEXP program to directly compare my
simulation results to experimental values. The program only can process
electron density profiles written as .dat and .sim files.

Is anyone aware of scripts or GROMACS options that will allow me to output
my electron density profile into a .dat or .sim file that can be processed
by SIMtoEXP?

Regards,
Sanim Rahman


You have the wrong program if you need electron densities.

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David van der Spoel, Ph.D., Professor of Biology
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