[gmx-users] GROMACS 5.1.0 crashes on pbs queue system

[Neha Gandhi]

Dear List,

I have compiled gromacs 5.1.0 using MPI. The job runs interactively as well
as through pbs submission using two nodes. However, the job crashes
immediately when I submit more than two jobs. Below is the error:
--
mpirun noticed that process rank 18 with PID 153374 on node
cl2n045.ib0.hpc.qut.edu.au exited on signal 4 (Illegal instruction).
--
24 total processes killed (some possibly by mpirun during cleanup)

-
PBS Job 1662894.pbs
CPU time  : 00:00:34
Wall time : 00:00:05
Mem usage : 256kb

Any input is much appreciated.

-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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[gmx-users] Doubt from topology creation using g_x2top

[Rakesh Pant]

Dear all,

I am trying to create a topology for a molecule using g_x2top and have
defined all the atoms with connectivity in *atomname.n2t* file with
different opls no. for all different types of atoms.

But when I create topology, it does not identify all different atomtypes
and takes one common opls no. for some of the atoms.

Thanks


Rakesh
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Re: [gmx-users] Regarding topology...

[Dilip H N]

Can anyone help me out kindly...regarding the previous error msg tht i have
got.



  Sent with Mailtrack


On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N 
wrote:

> Hello.. I have created a ammonia molecule... and i have CGennFF also...
> and thn in the terminal if i type gmx pdb2gmx -f ammonia.pdb -o
> ammonia.gro..and thn i enter for charmm36 force field...
> and thn none for water model since i  dnt want water (i just want to
> simulate ammonia)..
> and i am getting again residue AMM1 is not thr i rtp file entry..
> But Justin as u tld tht residue for ammonia is AMM1 and tht is in CGenFF...
> Can u rectify me whr the fault is..??
> below is the screen shot of both the terminal error msg and my pdb file
> with errors..
>
>
>
>   Sent with Mailtrack
> 
>
> On Tue, Feb 14, 2017 at 6:56 PM, Мижээ Батсайхан 
> wrote:
>
>> > --
>> >
>> > Message: 6
>> > Date: Tue, 14 Feb 2017 16:11:40 +0530
>> > From: Dilip H N 
>> > To: gmx-us...@gromacs.org
>> > Subject: Re: [gmx-users] Regarding topology...
>> > Message-ID:
>> > > > gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > How can i create a mixture of molecules and save it in .pdb format..?
>> > Is there any softwares for tht..?? or any software for pdb generator for
>> > gromacs..??
>> > Can anybody help...??
>> >
>> > you can use "gmx insert-molecules" (version 5 or later) for the mixture,
>> it needs pdb and topology files. you can use swissparam and prodrg server
>> etc. for generating topology depending on intended force field.
>>
>> I don't know any special pdb generator for gromacs, because there are many
>> software. what kind of system do you need?
>>
>> Regards,
>> Miji
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>>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student,
> Research Scholar,
> Department of Chemistry,
> National Institute of Technology-Karnataka,
> Surathkal, Mangaluru - 575025.
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.
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Re: [gmx-users] gmx gangle

[Antonio Baptista]

Hi João,

I used gangle to compute several angle distributions relative to the 
z-axis membrane normal, but that was almost a year ago, so I don't recall 
the details. But I can tell you that, after many failed attempts, I gave 
up from using fancy stuff in the -group1 and -group2 options. Instead, I 
ended up writing a small bash script to process one atom pair at a time 
(just one group in the .ndx file per gangle run) and to collect everything 
at the end.


I understand that your problem is a bit different (your second vector is 
not an axis, but defined by a second atom pair), but maybe a similar 
"minimalist" approach could get the job done. Or not... Good luck!


Best,
Antonio

On Wed, 15 Feb 2017, João Henriques wrote:


Hello everyone,

It seems that my inquiries about gmx gangle and selections are either too
funky or too basic to justify getting a single answer from the community.
Still, I will try once more with an even simpler scenario, which will
hopefully attract an answer (even if it's just someone telling me to stop
reposting, despite the fact that it is not 100% a repost).

I have a trajectory where the water molecules are ordered by proximity to
the protein. I also have an index file with the N closest waters that I am
interested in analyzing. Now, my plan is to simply compute the O-H angle
distribution within the group composed by these N water molecules. For that
I type something along these lines:

gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -g1 vector -group1 "group
"hydration_shell" and name OW HW1" -g2 vector -group2 "group
"hydration_shell" and name OW HW1" -oav -oall -oh

To my surprise, this command returns something completely different from
what I expected. Instead of the angular distribution function of all pairs
of O-H vectors from different water molecules, it outputs zero. Obviously,
this means that the command is computing the angle between the O-H vector
of each water molecule and itself. How can I modify my selection to produce
the desired result?

Thank you in advance,
Best regards,
João
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[gmx-users] gmx gangle

[João Henriques]

Hello everyone,

It seems that my inquiries about gmx gangle and selections are either too
funky or too basic to justify getting a single answer from the community.
Still, I will try once more with an even simpler scenario, which will
hopefully attract an answer (even if it's just someone telling me to stop
reposting, despite the fact that it is not 100% a repost).

I have a trajectory where the water molecules are ordered by proximity to
the protein. I also have an index file with the N closest waters that I am
interested in analyzing. Now, my plan is to simply compute the O-H angle
distribution within the group composed by these N water molecules. For that
I type something along these lines:

gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -g1 vector -group1 "group
"hydration_shell" and name OW HW1" -g2 vector -group2 "group
"hydration_shell" and name OW HW1" -oav -oall -oh

To my surprise, this command returns something completely different from
what I expected. Instead of the angular distribution function of all pairs
of O-H vectors from different water molecules, it outputs zero. Obviously,
this means that the command is computing the angle between the O-H vector
of each water molecule and itself. How can I modify my selection to produce
the desired result?

Thank you in advance,
Best regards,
João
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Re: [gmx-users] Drude-2013 FF, seg fault 11 on repeat minimization of beta-D-glucose monomer

[Justin Lemkul]

On 2/15/17 1:46 PM, Dayhoff, Guy wrote:

Hi,

   Thanks for taking the time to humor my inquiry.

I’m hoping to find a fix for my issue or obtain a working beta-D-glucose 
monomer model that I can use to
  continue troubleshooting my issue. Details below… (This is my first 
post, forgive me for including too much/
  too little context)

  My Best,
 Guy Dayhoff



   I am attempting to employ the Drude-2013FF available below to use with some 
carbohydrates:

 
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/drude-2013b_16sep2016.tgz

   I have obtained and installed the DRUDE compatible GROMACS distro available 
via:

 git clone git://git.gromacs.org/gromacs.git
 cd gromacs
git checkout drude

I am using pre-equilibrated SWM4-NDP water available from:

  
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/swm4-ndp_1024.gro

I have adjusted Drude parameters in my mdp files as demonstrated in the 
additional material from the publication
regarding implementation of the Drude FF and extended Lagrangian dynamics 
in GROMACS.

 Publication: http://dx.doi.org/10.1002/jcc.23937

 ; DRUDE PARAMETERS
drude = yes
 drude-mode = SCF
 drude-hyper = yes
 drude-khyp = 16736000.0
 drude-r = 0.02
 drude-pow = 4

I prepared a Drude model of beta-D-glucose(BGLC) to run before using more 
complex models by:

Downloading .CIF and .SDF data from RCSB-PDB @ https://www3.rcsb.org/ligand/BGC

Feeding this data into the CHARMM-GUI’s Ligand Reader & Modeler to produce .PDB 
and .PSF files

Feeding the .PDB and .PSF files into the CHARMM-GUI’s Drude Prepper producing 
bDgluc-Drude.pdb

I generated a topology file with pdb2gmx without any warnings/notes/errors:

gmx pdb2gmx -f bDgluc-Drude.pdb -o bDgluc-Drude.gro -p bDgluc-Drude.top

I placed the BGLC model in the center of a 3.0 x 3.0 x 3.0 box and 
minimized successfully:

gmx editconf -f bDgluc-Drude.gro -o bDgluc-Drude-CEN.gro -box 3.0 3.0 3.0 
-center 1.5 1.5 1.5

gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-CEN.gro -p 
bDgluc-Drude.top -o bDgluc-Drude-EMV.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMV

I then solvate the system and attempt to minimize it once more, this 
results in a seg fault 11:

gmx solvate -cp bDgluc-Drude-EMV.gro -cs swm4-ndp.gro -p bDgluc-Drude.top -o 
bDgluc-Drude-SOL.gro

gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-SOL.gro -p 
bDgluc-Drude.top -o bDgluc-Drude-EMS.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMS

Step=0, Dmax= 1.0e-02 nm, Epot=  nan Fmax= 3.77896e+06, atom= 16
Segmentation fault: 11

Likewise, if I simply take the minimized BGLC and attempt to minimize a 
second time I get the seg fault 11:

gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-EMV.gro -p 
bDgluc-Drude.top -o bDgluc-Drude-EMV2.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMV2

Step=0, Dmax= 1.0e-03 nm, Epot=  nan Fmax= 1.95057e+04, atom= 11
Segmentation fault: 11

I have attempted to isolate the cause and have noted:

  minimization and subsequent runs of a box of pure swm4-ndp produces no 
such errors, indicating the issue
is most likely related to the BGLC molecule in the system.

when beginning with a beta-D-glucose model not prepared with the CHARMM-GUI 
Drude Prepper (i.e. without
lone pairs and drudes included in the coordinate file) pdb2gmx properly 
adds all drudes, however fails to add
LP5A and LP5B, LPX5 is added though (CHARMM-GUI’s Drude Prepper doesn’t 
appear to have this issue).

using the -missing flag and proceeding with minimzation, solvation, NVT 
and NPT ensembles using the incomplete
model does not cause any seg faults and completes without errors.  In 
this case however, the molecule has a charge
(which corresponds exactly to the missing LP5A and LP5B).

with all things considered, I believe the issue lies with the handling of 
LP5A/LP5B in the BGLC residue in my model
but am unsure of how to proceed at this point.



It appears that LP5A and LP5B are missing from the .rtp definition so indeed 
they will not be built and the exclusions, etc. will be wrong.  I didn't test 
all the carbohydrates yet so I don't know why this occurred.


I'll look into it.

-Justin


the seg fault: 11 occurs on the first step of the minimizations

 My complete min.mdp for reference:

; PREPROCESSING
define   =

; RUN CONTROL
integrator= steep
nsteps= 1
dt   = 0.001
comm-mode= Linear
nstcomm = 1
nstcalcenergy = 1

; NEIGHBORSEARCHING
ns-type   = grid
rlist= 1.2
pbc = xyz
cutoff-scheme   = Verlet
periodic-molecules= no

; BONDS
constraints  = none
continuation  = no

; ELECTROSTATICS AND VDW
coulombtype  = PME
rcoulomb= 1.2
vdwtype   

[gmx-users] Drude-2013 FF, seg fault 11 on repeat minimization of beta-D-glucose monomer

[Dayhoff, Guy]

Hi,

   Thanks for taking the time to humor my inquiry.

I’m hoping to find a fix for my issue or obtain a working beta-D-glucose 
monomer model that I can use to
  continue troubleshooting my issue. Details below… (This is my first 
post, forgive me for including too much/
  too little context)

  My Best,
 Guy Dayhoff



   I am attempting to employ the Drude-2013FF available below to use with some 
carbohydrates:

 
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/drude-2013b_16sep2016.tgz

   I have obtained and installed the DRUDE compatible GROMACS distro available 
via:

 git clone git://git.gromacs.org/gromacs.git
 cd gromacs
git checkout drude

I am using pre-equilibrated SWM4-NDP water available from:

  
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/swm4-ndp_1024.gro

I have adjusted Drude parameters in my mdp files as demonstrated in the 
additional material from the publication
regarding implementation of the Drude FF and extended Lagrangian dynamics 
in GROMACS.

 Publication: http://dx.doi.org/10.1002/jcc.23937

 ; DRUDE PARAMETERS
drude = yes
 drude-mode = SCF
 drude-hyper = yes
 drude-khyp = 16736000.0
 drude-r = 0.02
 drude-pow = 4

I prepared a Drude model of beta-D-glucose(BGLC) to run before using more 
complex models by:

Downloading .CIF and .SDF data from RCSB-PDB @ https://www3.rcsb.org/ligand/BGC

Feeding this data into the CHARMM-GUI’s Ligand Reader & Modeler to produce .PDB 
and .PSF files

Feeding the .PDB and .PSF files into the CHARMM-GUI’s Drude Prepper producing 
bDgluc-Drude.pdb

I generated a topology file with pdb2gmx without any warnings/notes/errors:

gmx pdb2gmx -f bDgluc-Drude.pdb -o bDgluc-Drude.gro -p bDgluc-Drude.top

I placed the BGLC model in the center of a 3.0 x 3.0 x 3.0 box and 
minimized successfully:

gmx editconf -f bDgluc-Drude.gro -o bDgluc-Drude-CEN.gro -box 3.0 3.0 3.0 
-center 1.5 1.5 1.5

gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-CEN.gro -p 
bDgluc-Drude.top -o bDgluc-Drude-EMV.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMV

I then solvate the system and attempt to minimize it once more, this 
results in a seg fault 11:

gmx solvate -cp bDgluc-Drude-EMV.gro -cs swm4-ndp.gro -p bDgluc-Drude.top -o 
bDgluc-Drude-SOL.gro

gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-SOL.gro -p 
bDgluc-Drude.top -o bDgluc-Drude-EMS.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMS

Step=0, Dmax= 1.0e-02 nm, Epot=  nan Fmax= 3.77896e+06, atom= 16
Segmentation fault: 11

Likewise, if I simply take the minimized BGLC and attempt to minimize a 
second time I get the seg fault 11:

gmx grompp -v -f ../mdps/min.mdp -c bDgluc-Drude-EMV.gro -p 
bDgluc-Drude.top -o bDgluc-Drude-EMV2.tpr

gmx mdrun -v -deffnm bDgluc-Drude-EMV2

Step=0, Dmax= 1.0e-03 nm, Epot=  nan Fmax= 1.95057e+04, atom= 11
Segmentation fault: 11

I have attempted to isolate the cause and have noted:

  minimization and subsequent runs of a box of pure swm4-ndp produces no 
such errors, indicating the issue
is most likely related to the BGLC molecule in the system.

when beginning with a beta-D-glucose model not prepared with the CHARMM-GUI 
Drude Prepper (i.e. without
lone pairs and drudes included in the coordinate file) pdb2gmx properly 
adds all drudes, however fails to add
LP5A and LP5B, LPX5 is added though (CHARMM-GUI’s Drude Prepper doesn’t 
appear to have this issue).

using the -missing flag and proceeding with minimzation, solvation, NVT 
and NPT ensembles using the incomplete
model does not cause any seg faults and completes without errors.  In 
this case however, the molecule has a charge
(which corresponds exactly to the missing LP5A and LP5B).

with all things considered, I believe the issue lies with the handling of 
LP5A/LP5B in the BGLC residue in my model
but am unsure of how to proceed at this point.

the seg fault: 11 occurs on the first step of the minimizations

 My complete min.mdp for reference:

; PREPROCESSING
define   =

; RUN CONTROL
integrator= steep
nsteps= 1
dt   = 0.001
comm-mode= Linear
nstcomm = 1
nstcalcenergy = 1

; NEIGHBORSEARCHING
ns-type   = grid
rlist= 1.2
pbc = xyz
cutoff-scheme   = Verlet
periodic-molecules= no

; BONDS
constraints  = none
continuation  = no

; ELECTROSTATICS AND VDW
coulombtype  = PME
rcoulomb= 1.2
vdwtype = Cut-off
rvdw   = 1.2
DispCorr= EnerPres
vdw-modifier   = potential-switch
rvdw-switch   = 1.0

; ENERGY MINIMIZATION OPTIONS
emtol  = 10.0
emstep   = 0.001

; EWALD
fourierspacing 

Re: [gmx-users] Ris: position restraint single atom

[Justin Lemkul]

On 2/15/17 11:10 AM, Andrea Spitaleri wrote:

How Larger? I used 1000



No idea, but that's the first thing I'd try if using two atoms to resist the 
motion of thousands of others.


-Justin


 Messaggio originale 
Oggetto: Re: [gmx-users] position restraint single atom
Da: Justin Lemkul
A: gmx-us...@gromacs.org
CC:



On 2/15/17 9:33 AM, Andrea Spitaleri wrote:

Hi there,

I have a dsDNA and I'd like to restraint just two atoms, O3' and O5'
respectively, in order to mimic the anchor-like to a solid support. I have
create ad hoc posre.itp file but for some reason the DNA-anchor is moving too
much from the starting position. I would expect more rigidity around the two
atoms. Does it sound strange to you? I mean, I was expecting oscillation of the
whole DNA but keeping the anchors fixed. Are two atoms too little to get this
kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2.

Any help/comments on this are welcome.



What about using a larger force constant?  Trying to impede the motion of an
entire dsDNA using only two atoms as restraints might be difficult to 
accomplish.

-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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--
==

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] How treat PBC with -rerun option when simulate protein in a defined water shell?

[Juan José Galano Frutos]

Thanks Mark for your replay.

About the part where you say...

>The problem comes when one side of your shell can see
>the other across the gap within the cutoff, and you're still thinking of it
>as an isolated single shell

...yes, I agree with you that one must be aware about this issue. But about
the other aspect you pointed out:

>or if you're using PME, so that everything
>sees everything at long range

...I'm not so clear.

The point is we've used PME both in the original simulations and in the 'rerun'
ones (the .mdp files are almost idem). Then, what should we do here to
avoid this
problem? ...maybe to turn off the PME long-range electrostatics only
in the rerun
step? If so, wouldn't that importantly change results in terms of
Energy only by
the effect of changing the electrostatic treatment?
Another solution? ...maybe setting up a different electrostatics from
the begining
(the same both in the original simulations and in the rerun ones)?
What's treatment
we could use to get the longe-range electrostatics turned off without
loosing so
much accuracy in terms of Energy? ...'cut-off', 'PME-Switch' maybe? ... or a
coulomb-modifier such as Potential-shift-Verlet?

Any suggestion there, please?

Thanks a lot.


https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-February/111037.html

Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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Re: [gmx-users] Error select a group gmx_density

[Justin Lemkul]

On 2/15/17 11:18 AM, Poncho Arvayo Zatarain wrote:



Ok, thanks Justin. But i have one more question: What do you mean with syntax
make_ndx? Is the way the command is writting: gmx_gpu density -ng 4 -f
npt06.xtc -s npt06.tpr -o density.xvg? Is there anoher way to wrtie the
command for density?



My comment was not anything related to the command itself.  You were trying to 
use & and | operators to merge groups.  That's make_ndx syntax.  It's not 
something you can do with analysis tools.  Selections made (when choosing from a 
list of available groups) with analysis tools are done with a single number or 
group name.


-Justin


 De:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 en nombre de Justin
Lemkul  Enviado: miércoles, 15 de febrero de 2017 08:02 a.
m. Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Error select a group
gmx_density



On 2/15/17 10:55 AM, Poncho Arvayo Zatarain wrote:


Hello Gromacs users: I´m trying to obtain the density og a mixed membrane
plus a protein. I use the command line:  gmx_gpu density -ng 4 -f npt.xtc
-s npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION
5.0.4 (single precision)

Select 4 groups to calculate density for: Group 0 ( System)
has 58780 elements Group 1 (  Other) has 58780 elements Group
2 ( PROTEIN) has   576 elements Group 3 (   DPPC) has 16640
elements Group 4 (   DPPE) has 15488 elements Group 5 (
TIP3) has 26076 elements Select a group: 3 & 4 & 2 & 5 Selected 3: 'DPPC'
Select a group: Error: No such group '&' Select a group: Selected 4:
'DPPE' Select a group: Error: No such group '&' Select a group: Selected
2: 'PROTEIN' Select a group: Error: No such group '&' Select a group:
Selected 5: 'TIP3' Last frame   5000 time 21.000

Read 5001 frames from trajectory. Calculating density

Is there anything wrong with the command line or with Select a group:
Error: No such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the
same error but with | instead &? What about the Last frame 5000 time
21.000?


You can't use make_ndx style syntax with gmx density.  You should be
prompted for 4 selections, individually.  Otherwise, just calculate the
density of each group separately.


Why 5000 and not 21.000?. Also, and .xvg file is generated Thanks



What should the time be?  What is printed to the terminal is just a running
indicator of progress; it is not a definitive statement of the contents of
the trajectory.  For that, use gmx check (or look in the .xvg file to see the
time values).

-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
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]

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

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Re: [gmx-users] Error select a group gmx_density

[Poncho Arvayo Zatarain]

Ok, thanks Justin. But i have one more question: What do you mean with syntax 
make_ndx? Is the way the command is writting: gmx_gpu density -ng 4 -f 
npt06.xtc -s npt06.tpr -o density.xvg? Is there anoher way to wrtie the command 
for density?


De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 en nombre de Justin Lemkul 

Enviado: miércoles, 15 de febrero de 2017 08:02 a. m.
Para: gmx-us...@gromacs.org
Asunto: Re: [gmx-users] Error select a group gmx_density



On 2/15/17 10:55 AM, Poncho Arvayo Zatarain wrote:
>
> Hello Gromacs users: I´m trying to obtain the density og a mixed membrane
> plus a protein. I use the command line:  gmx_gpu density -ng 4 -f npt.xtc -s
> npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION 5.0.4
> (single precision)
>
> Select 4 groups to calculate density for: Group 0 ( System) has
> 58780 elements Group 1 (  Other) has 58780 elements Group 2 (
> PROTEIN) has   576 elements Group 3 (   DPPC) has 16640 elements
> Group 4 (   DPPE) has 15488 elements Group 5 (
> TIP3) has 26076 elements Select a group: 3 & 4 & 2 & 5 Selected 3: 'DPPC'
> Select a group: Error: No such group '&' Select a group: Selected 4: 'DPPE'
> Select a group: Error: No such group '&' Select a group: Selected 2:
> 'PROTEIN' Select a group: Error: No such group '&' Select a group: Selected
> 5: 'TIP3' Last frame   5000 time 21.000
>
> Read 5001 frames from trajectory. Calculating density
>
> Is there anything wrong with the command line or with Select a group: Error:
> No such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the same
> error but with | instead &? What about the Last frame 5000 time 21.000?

You can't use make_ndx style syntax with gmx density.  You should be prompted
for 4 selections, individually.  Otherwise, just calculate the density of each
group separately.

> Why 5000 and not 21.000?. Also, and .xvg file is generated Thanks
>

What should the time be?  What is printed to the terminal is just a running
indicator of progress; it is not a definitive statement of the contents of the
trajectory.  For that, use gmx check (or look in the .xvg file to see the time
values).

-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
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]

Welcome to my site! - University of Maryland, 
Baltimore
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.




==
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[gmx-users] Ris: position restraint single atom

[Andrea Spitaleri]

How Larger? I used 1000

 Messaggio originale 
Oggetto: Re: [gmx-users] position restraint single atom
Da: Justin Lemkul
A: gmx-us...@gromacs.org
CC:



On 2/15/17 9:33 AM, Andrea Spitaleri wrote:
> Hi there,
>
> I have a dsDNA and I'd like to restraint just two atoms, O3' and O5'
> respectively, in order to mimic the anchor-like to a solid support. I have
> create ad hoc posre.itp file but for some reason the DNA-anchor is moving too
> much from the starting position. I would expect more rigidity around the two
> atoms. Does it sound strange to you? I mean, I was expecting oscillation of 
> the
> whole DNA but keeping the anchors fixed. Are two atoms too little to get this
> kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2.
>
> Any help/comments on this are welcome.
>

What about using a larger force constant?  Trying to impede the motion of an
entire dsDNA using only two atoms as restraints might be difficult to 
accomplish.

-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] Error select a group gmx_density

[Justin Lemkul]

On 2/15/17 10:55 AM, Poncho Arvayo Zatarain wrote:


Hello Gromacs users: I´m trying to obtain the density og a mixed membrane
plus a protein. I use the command line:  gmx_gpu density -ng 4 -f npt.xtc -s
npt.tpr -o density.xvg. And this appears: Reading file npt.tpr, VERSION 5.0.4
(single precision)

Select 4 groups to calculate density for: Group 0 ( System) has
58780 elements Group 1 (  Other) has 58780 elements Group 2 (
PROTEIN) has   576 elements Group 3 (   DPPC) has 16640 elements
Group 4 (   DPPE) has 15488 elements Group 5 (
TIP3) has 26076 elements Select a group: 3 & 4 & 2 & 5 Selected 3: 'DPPC'
Select a group: Error: No such group '&' Select a group: Selected 4: 'DPPE'
Select a group: Error: No such group '&' Select a group: Selected 2:
'PROTEIN' Select a group: Error: No such group '&' Select a group: Selected
5: 'TIP3' Last frame   5000 time 21.000

Read 5001 frames from trajectory. Calculating density

Is there anything wrong with the command line or with Select a group: Error:
No such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the same
error but with | instead &? What about the Last frame 5000 time 21.000?


You can't use make_ndx style syntax with gmx density.  You should be prompted 
for 4 selections, individually.  Otherwise, just calculate the density of each 
group separately.



Why 5000 and not 21.000?. Also, and .xvg file is generated Thanks



What should the time be?  What is printed to the terminal is just a running 
indicator of progress; it is not a definitive statement of the contents of the 
trajectory.  For that, use gmx check (or look in the .xvg file to see the time 
values).


-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] position restraint single atom

[Justin Lemkul]

On 2/15/17 9:33 AM, Andrea Spitaleri wrote:

Hi there,

I have a dsDNA and I'd like to restraint just two atoms, O3' and O5'
respectively, in order to mimic the anchor-like to a solid support. I have
create ad hoc posre.itp file but for some reason the DNA-anchor is moving too
much from the starting position. I would expect more rigidity around the two
atoms. Does it sound strange to you? I mean, I was expecting oscillation of the
whole DNA but keeping the anchors fixed. Are two atoms too little to get this
kind behaviour (i.e. DNA-anchor)? The constant force is 1000 kJ/mol nm^2.

Any help/comments on this are welcome.



What about using a larger force constant?  Trying to impede the motion of an 
entire dsDNA using only two atoms as restraints might be difficult to accomplish.


-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] Error select a group gmx_density

[Poncho Arvayo Zatarain]

Hello Gromacs users: I´m trying to obtain the density og a mixed membrane plus 
a protein. I use the command line:  gmx_gpu density -ng 4 -f npt.xtc -s npt.tpr 
-o density.xvg. And this appears:
Reading file npt.tpr, VERSION 5.0.4 (single precision)

Select 4 groups to calculate density for:
Group 0 ( System) has 58780 elements
Group 1 (  Other) has 58780 elements
Group 2 (PROTEIN) has   576 elements
Group 3 (   DPPC) has 16640 elements
Group 4 (   DPPE) has 15488 elements
Group 5 (   TIP3) has 26076 elements
Select a group: 3 & 4 & 2 & 5
Selected 3: 'DPPC'
Select a group: Error: No such group '&'
Select a group: Selected 4: 'DPPE'
Select a group: Error: No such group '&'
Select a group: Selected 2: 'PROTEIN'
Select a group: Error: No such group '&'
Select a group: Selected 5: 'TIP3'
Last frame   5000 time 21.000

Read 5001 frames from trajectory. Calculating density

Is there anything wrong with the command line or with Select a group: Error: No 
such group '&'? Also i tried with 3 | 4 | | 2 | 5 and appears the same error 
but with | instead &? What about the Last frame 5000 time 21.000? Why 5000 
and not 21.000?. Also, and .xvg file is generated
Thanks

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[gmx-users] position restraint single atom

[Andrea Spitaleri]

Hi there,

I have a dsDNA and I'd like to restraint just two atoms, O3' and O5' 
respectively, in order to mimic the anchor-like to a solid support. I 
have create ad hoc posre.itp file but for some reason the DNA-anchor is 
moving too much from the starting position. I would expect more rigidity 
around the two atoms. Does it sound strange to you? I mean, I was 
expecting oscillation of the whole DNA but keeping the anchors fixed. 
Are two atoms too little to get this kind behaviour (i.e. DNA-anchor)? 
The constant force is 1000 kJ/mol nm^2.


Any help/comments on this are welcome.

Thanks

and


--
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/-0003-3012-3557

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[gmx-users] position restraint single atom

[Andrea Spitaleri]

Hi there,

I have a dsDNA and I'd like to restraint just two atoms, O3' and O5' 
respectively, in order to mimic the anchor-like to a solid support. I 
have create ad hoc posre.itp file but for some reason the DNA-anchor is 
moving too much from the starting position. I would expect more rigidity 
around the two atoms. Does it sound strange to you? I mean, I was 
expecting oscillation of the whole DNA but keeping the anchors fixed. 
Are two atoms too little to get this kind behaviour (i.e. DNA-anchor)? 
The constant force is 1000 kJ/mol nm^2.


Any help/comments on this are welcome.

Thanks

and


--
Andrea Spitaleri PhD
Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab
ISTITUTO ITALIANO DI TECNOLOGIA
Via Morego 30, 16163 - Genova, Italy
https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems
cell: +39 3485188790
https://iit.it/andrea-spitaleri
ORCID: http://orcid.org/-0003-3012-3557

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Re: [gmx-users] How treat PBC with -rerun option when simulate protein in a defined water shell?

[Mark Abraham]

Hi,

The energies are well defined, either way. (Whether they'll be useful is
another matter...) The problem comes when one side of your shell can see
the other across the gap within the cutoff, and you're still thinking of it
as an isolated single shell. Of if you're using PME, so that everything
sees everything at long range. Using no PBC and infinite cutoff is at least
cleanly defined (but not yet implemented in the Verlet scheme).

Mark

On Wed, Feb 15, 2017 at 2:36 PM Juan José Galano Frutos 
wrote:

> Hi there,
>
> We are doing simulation in which we are interested in studying Energies,
> Enthalpies, etc. changes in systems with increasingly water shells around a
> protein. In this sense, we first extract bulk waters in order to leave the
> mentioned water shells with a defined radius around the protein. Then we do
> a rerun in order to recalculate the system energies, but my doubt here is:
> what exactly to do with PBC in the .mdp file? My doubts here come up
> because the system now (protein + water shell) is not a geometric box like
> a dodecahedron or a cubic box, and I am afraid about whether the energies I
> am obtaining are totally wrong. Do you think it will be better here not to
> use PBC or you think there is no matter in doing the rerun keeping PBC on?
> I guess that keeping PBC on, there will be some empty space between each
> side box (the space left by water removed), so I feel it could be important
> ...
>
> Thank you very much.
>
>
> Juan José Galano Frutos
>
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Faculty of Sciences,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza (Spain)
> +34 976 76 28 06 <+34%20976%2076%2028%2006>
>
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
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Re: [gmx-users] Too many error at first step

[Mark Abraham]

Hi,

You chose a force field capable of describing the protein + Mg ion. Well
done. Whether that will be a good model of physics of your system remains
to be seen. I would strongly suggest finding a different problem for your
first MD study. There are far too many errors to make without needing to
deal with doubtful metal parameters, or modified ligands. Learn to walk
before trying to run juggling knives!

Mark

On Wed, Feb 15, 2017 at 2:25 PM Chintan Bhagat 
wrote:

> Dear Justin,
>
> Thank you for your reply.
>
> I selected my protein for MD study and I did the stimulation same as
> mentioned in  lysozyme tutorial *using force field - GROMOS96 43a1 force
> field *(As, I came to know all force field has different .mdp file, so
> results are not vaild). I did the same as mention in tutorial (using .mdp
> fie). But, When i selected  OPLS-AA/L all-atom force field, I got error
> message,* Residue 'ZN' not found in residue topology database*.
>
> Later, I search on literature, I found chaining ZN to MG is good and will
> does not make any significance changes in result. So, I replaced ZN by MG
> in my file and run the stimulation using OPLS-AA/L all-atom force field (
>
> https://www.researchgate.net/post/How_can_I_rectify_this_error_Atom_type_Zn2_residue_ZN_not_found_in_atomtype_database
> ).
> This time, I did not got any error or warning message. As, I  am new, I am
> not sure, I am doing right or not .
>
> I also search for for adding residue to force field file, but not able do
> well (
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> ).
>
>
> I request you to suggest me whether I am doing right or not? (As, I am not
> expert!!)
>
> hope you reply.
>
> On Mon, Jan 30, 2017 at 10:29 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 1/30/17 11:54 AM, Chintan Bhagat wrote:
> >
> >> Hello Justin,
> >>
> >> Which force field should I use?
> >>
> >
> > One that supports what you need.  I don't mean that to be dismissive;
> it's
> > your job in designing your research to look at the pros and cons of each
> > force field, and no one can or should make that (very critical) decision
> > for you.  Has it been demonstrated to be effective for similar systems?
> > What are the limitations?
> >
> > Further, How to check the compatibility of protein for force field? PDB
> id
> >> of my protein is 4g7a.
> >>
> >
> > The protein isn't the issue.  Every force field in GROMACS will handle
> the
> > protein.  But Zn is another matter.  This again requires an investigation
> > and assessment of the literature.
> >
> > Secondly, I am using Gromacs VERSION 5.1.4 which is most updated.
> >>
> >>
> > No, version 2016.1 is the latest, and I personally fixed the bug I
> > referred to for this version after 5.1.4 was released.  Trust me, I'm
> > trying to help you avoid a very serious serious bug :)
> >
> > -Justin
> >
> > Thanking you,
> >> Chinatn
> >>
> >>
> >>
> >>   Sent with Mailtrack
> >>  >> ral=cbb.chin...@gmail.com&idSignature=22>
> >>
> >>
> >> On Mon, Jan 30, 2017 at 9:45 PM, Justin Lemkul  wrote:
> >>
> >>
> >>>
> >>> On 1/30/17 11:08 AM, Chintan Bhagat wrote:
> >>>
> >>> Hello all,
> 
>  I am new to Gromacs, and I completed the Lysozyme tutorial. But When I
>  started stimulation with my own protein, I got many errors. I am not
>  understanding what to do?
> 
>  For error
>  
>  -
> 
>  lab@lab-desktop:~/Desktop/MD_tutorial$ gmx pdb2gmx -f 4g7a.pdb -o
>  4g7a_processed.gro -water spce
>  .
>  .
>  .
>  .
>  .
>  
>  gmx pdb2gmx -f 4g7a.pdb -o 4g7a_processed.gro -water spce
> 
> 
>  Select the Force Field:
>  From '/usr/local/gromacs/share/gromacs/top':
>  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
>  1999-2012, 2003)
>  2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>  3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res.
> 29,
>  461-469, 1996)
>  4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
>  1049-1074, 2000)
>  5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
>  712-725,
>  2006)
>  6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
>  Proteins 78, 1950-58, 2010)
>  7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787,
> 2002)
>  8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>  9: GROMOS96 43a1 force field
>  10: GROMOS96 43a2 force field (improved alkane dihedrals)
>  11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>  12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>  13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>  14: GROMOS96 54a7

[gmx-users] How treat PBC with -rerun option when simulate protein in a defined water shell?

[Juan José Galano Frutos]

Hi there,

We are doing simulation in which we are interested in studying Energies,
Enthalpies, etc. changes in systems with increasingly water shells around a
protein. In this sense, we first extract bulk waters in order to leave the
mentioned water shells with a defined radius around the protein. Then we do
a rerun in order to recalculate the system energies, but my doubt here is:
what exactly to do with PBC in the .mdp file? My doubts here come up
because the system now (protein + water shell) is not a geometric box like
a dodecahedron or a cubic box, and I am afraid about whether the energies I
am obtaining are totally wrong. Do you think it will be better here not to
use PBC or you think there is no matter in doing the rerun keeping PBC on?
I guess that keeping PBC on, there will be some empty space between each
side box (the space left by water removed), so I feel it could be important
...

Thank you very much.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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Re: [gmx-users] Too many error at first step

[Chintan Bhagat]

Dear Justin,

Thank you for your reply.

I selected my protein for MD study and I did the stimulation same as
mentioned in  lysozyme tutorial *using force field - GROMOS96 43a1 force
field *(As, I came to know all force field has different .mdp file, so
results are not vaild). I did the same as mention in tutorial (using .mdp
fie). But, When i selected  OPLS-AA/L all-atom force field, I got error
message,* Residue 'ZN' not found in residue topology database*.

Later, I search on literature, I found chaining ZN to MG is good and will
does not make any significance changes in result. So, I replaced ZN by MG
in my file and run the stimulation using OPLS-AA/L all-atom force field (
https://www.researchgate.net/post/How_can_I_rectify_this_error_Atom_type_Zn2_residue_ZN_not_found_in_atomtype_database).
This time, I did not got any error or warning message. As, I  am new, I am
not sure, I am doing right or not .

I also search for for adding residue to force field file, but not able do
well (
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field).


I request you to suggest me whether I am doing right or not? (As, I am not
expert!!)

hope you reply.

On Mon, Jan 30, 2017 at 10:29 PM, Justin Lemkul  wrote:

>
>
> On 1/30/17 11:54 AM, Chintan Bhagat wrote:
>
>> Hello Justin,
>>
>> Which force field should I use?
>>
>
> One that supports what you need.  I don't mean that to be dismissive; it's
> your job in designing your research to look at the pros and cons of each
> force field, and no one can or should make that (very critical) decision
> for you.  Has it been demonstrated to be effective for similar systems?
> What are the limitations?
>
> Further, How to check the compatibility of protein for force field? PDB id
>> of my protein is 4g7a.
>>
>
> The protein isn't the issue.  Every force field in GROMACS will handle the
> protein.  But Zn is another matter.  This again requires an investigation
> and assessment of the literature.
>
> Secondly, I am using Gromacs VERSION 5.1.4 which is most updated.
>>
>>
> No, version 2016.1 is the latest, and I personally fixed the bug I
> referred to for this version after 5.1.4 was released.  Trust me, I'm
> trying to help you avoid a very serious serious bug :)
>
> -Justin
>
> Thanking you,
>> Chinatn
>>
>>
>>
>>   Sent with Mailtrack
>> > ral=cbb.chin...@gmail.com&idSignature=22>
>>
>>
>> On Mon, Jan 30, 2017 at 9:45 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 1/30/17 11:08 AM, Chintan Bhagat wrote:
>>>
>>> Hello all,

 I am new to Gromacs, and I completed the Lysozyme tutorial. But When I
 started stimulation with my own protein, I got many errors. I am not
 understanding what to do?

 For error
 
 -

 lab@lab-desktop:~/Desktop/MD_tutorial$ gmx pdb2gmx -f 4g7a.pdb -o
 4g7a_processed.gro -water spce
 .
 .
 .
 .
 .
 
 gmx pdb2gmx -f 4g7a.pdb -o 4g7a_processed.gro -water spce


 Select the Force Field:
 From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
 1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
 461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
 1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
 712-725,
 2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
 Proteins 78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
 10: GROMOS96 43a2 force field (improved alkane dihedrals)
 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856,
 DOI:
 10.1007/s00249-011-0700-9)
 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
 15

 Using the Oplsaa force field in directory oplsaa.ff

 Opening force field file
 /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
 Reading 4g7a.pdb...

 *WARNING: all CONECT records are ignored*
 Read 'CARBONATE DEHYDRATASE', 3726 atoms
 Analyzing pdb file
 Splitting chemical chains based on TER records or chain id changing.

 *WARNING: Chain identifier 'A' is used in two non-sequential blocks*.
 They will be treated as separate chains unless you reorder your file.

 *WARN