[gmx-users] H definition in urea topology file buildup

[Divya Dube]

Dear All,

There are four hydrogen atoms in urea molecule for which I have made H
atoms definition in aminoacids.hdb file.

URE4
13H11N1CN2
13H12N1CN2
13H21N2CN1
13H22N2CN1

Still pdb2gmx is unable in recognizing these H atoms and giving error.
Can anyone suggest the correct way of defining urea in HDb file


regards
Divya
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[gmx-users] gromacs on multiple gpus

[Neha Gandhi]

Dear List,

I have compiled GROMACS 5.0.7 using following options

CMAKE_PREFIX_PATH=/home/gandhin/fftw cmake .. -DGMX_BUILD_OWN_FFTW=OFF
-DGMX_MPI=on -DGMX_GPU=on -DGMX_SIMD=AVX2_256
-DCMAKE_C_COMPILER=${MPICCDIR}mpicc -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx
-DGMX_BUILD_MDRUN_ONLY=on -DCMAKE_INSTALL_PREFIX=/home/gandhin/gromacs-5.0.7

The machine has two K40 gpus and 12 cpus per node. When I submit jobs using
mpirun gmx_mpi mdrun -v.. the program mdrun detects two gpus with ids #0
and #1 but it still runs the job with only one gpu i.e. gpu id #0. What is
the correct way of submitting job (using PBS) so that both gpus and 12
cores on the same node are utilised by mdrun for the simulation?

My apologies to post this question to GROMACS mailing list, this post is
more related to the system admin who aren't able to help.

Thank you for kind attention

Regards,
Neha





-- 
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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Re: [gmx-users] Convert gro into psf

[Roshan Shrestha]

I am extremely sorry that I did not provide full command, the command is-
gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p topol.top -ignh -v where I chose
charmm27 for force field and tip3p for water model.
On 10 May 2016 8:39 am, "Roshan Shrestha"  wrote:

> Is it possible to convert .gro file into. psf file ?
> I am finding it tough to create psf file for 6pti.pdb using NAMD. So, Can
> I convert say bpti.gro into bpti.psf where I produced bpti.gro using
> command gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p
>
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[gmx-users] Convert gro into psf

[Roshan Shrestha]

Is it possible to convert .gro file into. psf file ?
I am finding it tough to create psf file for 6pti.pdb using NAMD. So, Can I
convert say bpti.gro into bpti.psf where I produced bpti.gro using command
gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p
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Re: [gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

[Pedro Lacerda]

Yes, GromacsWrapper doesn't enforces some project structure, it's more like
a library despite its name.
GmxScript enforces some kind of project organization. As GromacsWrapper,
it's not a huge advantage over pure shell scripts, except because every
command is checkpointed and is very readable.

Cheers,
Pedro Lacerda

2016-05-07 0:06 GMT-03:00 Peter Stern :

> I guess that Pedro clearly knows that since he refers to it on his page
> and explains why his is different.
>
> Cheers,
> Peter
>
> Sent from my iPad
>
> > On May 6, 2016, at 12:22 PM, João M. Damas  wrote:
> >
> > There is already a similar project going on for a long time:
> > https://orbeckst.github.io/GromacsWrapper/
> >
> > Cheers,
> > João
> >
> > On Wed, May 4, 2016 at 3:12 AM, Pedro Lacerda 
> > wrote:
> >
> >> Installation is now working. The upload script was broken.
> >>
> >> 2016-05-03 21:50 GMT-03:00 Pedro Lacerda :
> >>
> >>> Hi Gromacs users,
> >>>
> >>> I just started to develop a scripting framework for Gromacs, it makes
> >> some
> >>> assumptions about the directory structure and command parameters. You
> >>> cannot prepare or run two different systems in the same directory and
> >>> always pass the -deffnm option to mdrun.
> >>>
> >>> It is very nice!
> >>>
> >>> Its main goal is to easy the reproduction of simulation protocols,
> >>> canonical steps used to perform and analyze a simulation. The commands
> >> are
> >>> stored in very readable and structured Python file that requires no
> >>> programming knowledge except syntax. Of course you can always extend it
> >>> with code as you need.
> >>>
> >>> As a bonus it maintain in the .gmx/ directory a checkpoint file that
> skip
> >>> previously successful commands if started again. Also there is no need
> to
> >>> source GMXRC in common cases.
> >>>
> >>>https://github.com/pslacerda/gmx
> >>>
> >>> Please make comments, suggestions and critics about GMXSCRIPT. The next
> >>> feature would be an option to generate a file that allows to reproduce
> a
> >>> simulation in any linux computer with Gromacs installed.
> >>>
> >>> (apologies for my poor English!)
> >>>
> >>> Best regards,
> >>> Pedro Lacerda
> >> --
> >> 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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> >
> >
> >
> > --
> > João M. Damas
> > PhD Student
> > Protein Modelling Group
> > ITQB-UNL, Oeiras, Portugal
> > Tel:+351-214469613
> > --
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Re: [gmx-users] residue UNK not found- how to generate force field parameters?

[Justin Lemkul]

On 5/9/16 8:21 PM, Jacob Nowatzke wrote:

I want to take a fatty acid amide, oleamide, and toss it around in a
bilayer, eventually.

Right now, I am fine with solvating oleamide in water, just to get to that
point would be wonderful.

The title captures my issue- I don't know how to generate proper force
field parameters and implement them in GROMACS- I can find no definitive
walk-through on the issue, and it seems some older GROMACS web pages are no
longer available.

May I ask the community for any leads on a simplified overview of how to
generate proper topology for a compound such as oleamide, to implement said
compound into GROMACS MD simulations?

I am sure my lack of expertise shows- I'm aware I am out of my league,
however if I can walk through tutorials, there's not much reason I can't
branch out to use my own choice of ligands/non-proteins after learning how
to generate these needed definitions.

Any help is greatly appreciated. My end goal for oleamide is simply a MD
simulation with annealing from 310K to ~275K, over a varying time frame.
Right now, of course, I'm concerned with getting past residue 'UNK'.



Oleamide should be very straightforward to put together based on available 
parameters (you haven't said which force field you want to use, but they should 
all support it).  Models in additive force fields are typically built by piecing 
together building blocks, here an amide (e.g. Asn/Gln side chain) and an alkyl 
chain that has an unsaturation.  Pretty straightforward.  You'll need to consult 
both theoretical and experimental literature to find/generate suitable target 
data for validation; this is why there are few, if any, full tutorials on 
parametrization.  It's very difficult to find a robust example that has lots of 
useful data for it.


Once you have some initial parameters, abandon these generic "UNK" labels and 
name your residue something sensible.  The incorporate it into an .rtp entry and 
follow 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field


It's rather straightforward to add a residue; what's more difficult is obviously 
coming up with the parameters, but that's not a GROMACS issue per se.


-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] residue UNK not found- how to generate force field parameters?

[Jacob Nowatzke]

I want to take a fatty acid amide, oleamide, and toss it around in a
bilayer, eventually.

Right now, I am fine with solvating oleamide in water, just to get to that
point would be wonderful.

The title captures my issue- I don't know how to generate proper force
field parameters and implement them in GROMACS- I can find no definitive
walk-through on the issue, and it seems some older GROMACS web pages are no
longer available.

May I ask the community for any leads on a simplified overview of how to
generate proper topology for a compound such as oleamide, to implement said
compound into GROMACS MD simulations?

I am sure my lack of expertise shows- I'm aware I am out of my league,
however if I can walk through tutorials, there's not much reason I can't
branch out to use my own choice of ligands/non-proteins after learning how
to generate these needed definitions.

Any help is greatly appreciated. My end goal for oleamide is simply a MD
simulation with annealing from 310K to ~275K, over a varying time frame.
Right now, of course, I'm concerned with getting past residue 'UNK'.

Thank you!
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[gmx-users] memory error

[Clinton King]

Does anyone know how to change the memory allocated to the QM part of a
QM/MM calculation?

I'm using the gau script linked to on this page
http://wwwuser.gwdg.de/~ggroenh/qmmm.html to connect to Gaussian 09

I'm setting a header to allocate 8 GB of memory and 8 processors to
Gaussian, but in the output I see this message:

"number of CPUs for gaussian = 1
memory for gaussian = 5000"

and then I get a memory error.

I don't see any description of keywords in the manual to set the memory in
the mdp file, but maybe I'm missing something. Does anybody have any ideas?
Thanks.


--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
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[gmx-users] Minimization of Cyclohexane Trappe United Atom

[doerrstein]

Dear Gromacs-Users,


I am trying to simulate Cyclohexane in the NpT-ensemble with the 
Trappe-UA model. So I needed to create my own
ff-folder, where I converted the Trappe-Parameters to 
Gromacs-Parameters. I tried it for molecules like
hexane, pentane and neopentane and for all of them I get quite 
reasonable results. Unfortunately when I try to
minimize united atom cyclohexane, the C-C-C-angles change from 111 
degrees to 100 degrees, which is quite questionable. When I change
the angles in my force-field-folder from 114 to 144 degress the C-C-C 
angles stay approximately at the starting value. After equilibration and 
production the angles

changes, but most of them do not reach

Most of the Trappe-folder is copied from Wes Barnetts website: 
https://github.com/wesbarnett/trappeua


Here is the link with my data: 
https://www.dropbox.com/sh/6y33co2vf9v9fex/AABfpndhgYsUUBpkAyJrhhKLa?dl=0




Maybe someone could give me some advice why this happens and how to 
avoid this problem. Should I worry about this at all?
After equilibration and production runs the angles changes, but most of 
them are still are quite far away from 111 or 114 degrees.


Many thanks in advance...

Best regards,
Mark
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[gmx-users] GPU/CPU perfomance loss

[Van Zyl, J, Mnr <justi...@sun.ac.za>]

Good day,


I am running simulations from a workstation and keep getting a gromacs note at 
the end of the run saying "The GPU has >25% less load than the CPU. This 
imbalance causes performance loss."


I have read a previous post pertaining to this problem but the only thing that 
seems to increase performance is by changing nstlist from 150 to 20 however the 
gromacs note still shows. I will post the log file of that run soon however 
below is the log file of the first run:

http://pastebin.com/3CUDh960


Is there anything I can do to increase perfomance or is this simply as good as 
it will get for my system (22467 atoms)?


Thanks for the help,

Regards,

Justin van Zyl

[http://pastebin.com/i/facebook.png]

md_1.log - Pastebin.com
pastebin.com




Justin van Zyl
MSc. Candidate
Department of Chemistry and Polymer Science,
Stellenbosch University, Private Bag X1 Matieland,
7602, South Africa
Cell: +27 72 9372 755
justi...@sun.ac.za
http://www.klumperman-group.net/

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[gmx-users] force calculation

[mahdiyeh poorsargol]

Dear Justin
Thank you for your reply
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Re: [gmx-users] invalid order of directive atomtypes

[Justin Lemkul]

On 5/9/16 11:16 AM, Brett wrote:

Dear All,

Will you please tell me why I got "invalid order of directive atomtypes?



Please avail yourself of the very comprehensive Errors page:

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

-Justin


Brett

Part of my itp was as following,

; ADP_BwithH_ADPBfine.itp created by acpype (Rev: 401) on Thu May  5 09:25:01 
2016
[atomtypes]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 oo   0.0  0.0   A 2.95992e-01   8.78640e-01 ; 1.66 
 0.2100
 p5   p5  0.0  0.0   A 3.74177e-01   8.36800e-01 ; 2.10 
 0.2000
 os   os  0.0  0.0   A 3.1e-01   7.11280e-01 ; 1.68 
 0.1700
 c3   c3  0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094
 oh   oh  0.0  0.0   A 3.06647e-01   8.80314e-01 ; 1.72 
 0.2104
 na   na  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 ca   ca  0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 nc   nc  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 cd   cd  0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 nb   nb  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 nh   nh  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 ho   ho  0.0  0.0   A 0.0e+00   0.0e+00 ; 0.00 
 0.
 hn   hn  0.0  0.0   A 1.06908e-01   6.56888e-02 ; 0.60 
 0.0157
 h1   h1  0.0  0.0   A 2.47135e-01   6.56888e-02 ; 1.39 
 0.0157
 h5   h5  0.0  0.0   A 2.42146e-01   6.27600e-02 ; 1.36 
 0.0150
 h2   h2  0.0  0.0   A 2.29317e-01   6.56888e-02 ; 1.29 
 0.0157

[ moleculetype ]
;namenrexcl
 ADPBfine3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
 1o 1   ADP   O2A1-0.947401 16.0 ; qtot -0.947
 2   p5 1   ADPPA2 1.492904 30.97000 ; qtot 0.546
 3o 1   ADP   O1A3-0.947401 16.0 ; qtot -0.402
 4   os 1   ADP   O3A4-0.634601 16.0 ; qtot -1.036
 5   p5 1   ADPPB5 1.367201 30.97000 ; qtot 0.331
 6o 1   ADP   O1B6-0.955201 16.0 ; qtot -0.624
 7o 1   ADP   O2B7-0.955201 16.0 ; qtot -1.580
 8o 1   ADP   O3B8-0.955201 16.0 ; qtot -2.535
 9   os 1   ADP   O5'9-0.657901 16.0 ; qtot -3.193
10   c3 1   ADP   C5'   10 0.055800 12.01000 ; qtot -3.137
11   c3 1   ADP   C4'   11 0.106500 12.01000 ; qtot -3.031
12   c3 1   ADP   C3'   12 0.202200 12.01000 ; qtot -2.828
13   oh 1   ADP   O3'   13-0.654101 16.0 ; qtot -3.482
14   c3 1   ADP   C2'   14 0.067000 12.01000 ; qtot -3.415
15   oh 1   ADP   O2'   15-0.613901 16.0 ; qtot -4.029
16   c3 1   ADP   C1'   16 0.039400 12.01000 ; qtot -3.990
17   os 1   ADP   O4'   17-0.354800 16.0 ; qtot -4.345

Par of my topl file was as following,
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"


; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_C.itp"
#include "topol_Protein_chain_D.itp"
#include "topol_Protein_chain_E.itp"
#include "topol_Protein_chain_F.itp"
#include "topol_Protein_chain_G.itp"
#include "topol_Protein_chain_H.itp"
#include "topol_Protein_chain_I.itp"
#include "topol_Protein_chain_J.itp"
#include "topol_Protein_chain_K.itp"
#include "topol_Protein_chain_L.itp"
#include "topol_Protein_chain_M.itp"
#include "topol_Protein_chain_N.itp"

; Include ligand topology
#include "ADPBfine.itp"

; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
Protein_chain_G 1
Protein_chain_H 1
Protein_chain_I 1
Protein_chain_J 1
Protein_chain_K 1
Protein_chain_L 1
Protein_chain_M 1
Protein_chain_N 1
ADPBfine   1



--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 

[gmx-users] invalid order of directive atomtypes

[Brett]

Dear All, 

Will you please tell me why I got "invalid order of directive atomtypes?

Brett

Part of my itp was as following,

; ADP_BwithH_ADPBfine.itp created by acpype (Rev: 401) on Thu May  5 09:25:01 
2016
[atomtypes]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 oo   0.0  0.0   A 2.95992e-01   8.78640e-01 ; 1.66 
 0.2100
 p5   p5  0.0  0.0   A 3.74177e-01   8.36800e-01 ; 2.10 
 0.2000
 os   os  0.0  0.0   A 3.1e-01   7.11280e-01 ; 1.68 
 0.1700
 c3   c3  0.0  0.0   A 3.39967e-01   4.57730e-01 ; 1.91 
 0.1094
 oh   oh  0.0  0.0   A 3.06647e-01   8.80314e-01 ; 1.72 
 0.2104
 na   na  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 ca   ca  0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 nc   nc  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 cd   cd  0.0  0.0   A 3.39967e-01   3.59824e-01 ; 1.91 
 0.0860
 nb   nb  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 nh   nh  0.0  0.0   A 3.25000e-01   7.11280e-01 ; 1.82 
 0.1700
 ho   ho  0.0  0.0   A 0.0e+00   0.0e+00 ; 0.00 
 0.
 hn   hn  0.0  0.0   A 1.06908e-01   6.56888e-02 ; 0.60 
 0.0157
 h1   h1  0.0  0.0   A 2.47135e-01   6.56888e-02 ; 1.39 
 0.0157
 h5   h5  0.0  0.0   A 2.42146e-01   6.27600e-02 ; 1.36 
 0.0150
 h2   h2  0.0  0.0   A 2.29317e-01   6.56888e-02 ; 1.29 
 0.0157

[ moleculetype ]
;namenrexcl
 ADPBfine3

[ atoms ]
;   nr  type  resi  res  atom  cgnr charge  mass   ; qtot   
bond_type
 1o 1   ADP   O2A1-0.947401 16.0 ; qtot -0.947
 2   p5 1   ADPPA2 1.492904 30.97000 ; qtot 0.546
 3o 1   ADP   O1A3-0.947401 16.0 ; qtot -0.402
 4   os 1   ADP   O3A4-0.634601 16.0 ; qtot -1.036
 5   p5 1   ADPPB5 1.367201 30.97000 ; qtot 0.331
 6o 1   ADP   O1B6-0.955201 16.0 ; qtot -0.624
 7o 1   ADP   O2B7-0.955201 16.0 ; qtot -1.580
 8o 1   ADP   O3B8-0.955201 16.0 ; qtot -2.535
 9   os 1   ADP   O5'9-0.657901 16.0 ; qtot -3.193
10   c3 1   ADP   C5'   10 0.055800 12.01000 ; qtot -3.137
11   c3 1   ADP   C4'   11 0.106500 12.01000 ; qtot -3.031
12   c3 1   ADP   C3'   12 0.202200 12.01000 ; qtot -2.828
13   oh 1   ADP   O3'   13-0.654101 16.0 ; qtot -3.482
14   c3 1   ADP   C2'   14 0.067000 12.01000 ; qtot -3.415
15   oh 1   ADP   O2'   15-0.613901 16.0 ; qtot -4.029
16   c3 1   ADP   C1'   16 0.039400 12.01000 ; qtot -3.990
17   os 1   ADP   O4'   17-0.354800 16.0 ; qtot -4.345

Par of my topl file was as following,
; Include forcefield parameters
#include "amber99sb-ildn.ff/forcefield.itp"


; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_C.itp"
#include "topol_Protein_chain_D.itp"
#include "topol_Protein_chain_E.itp"
#include "topol_Protein_chain_F.itp"
#include "topol_Protein_chain_G.itp"
#include "topol_Protein_chain_H.itp"
#include "topol_Protein_chain_I.itp"
#include "topol_Protein_chain_J.itp"
#include "topol_Protein_chain_K.itp"
#include "topol_Protein_chain_L.itp"
#include "topol_Protein_chain_M.itp"
#include "topol_Protein_chain_N.itp"

; Include ligand topology
#include "ADPBfine.itp"

; Include water topology
#include "amber99sb-ildn.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "amber99sb-ildn.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
Protein_chain_G 1
Protein_chain_H 1
Protein_chain_I 1
Protein_chain_J 1
Protein_chain_K 1
Protein_chain_L 1
Protein_chain_M 1
Protein_chain_N 1
ADPBfine   1

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[gmx-users] qm/mm

[Jacopo Sgrignani]

Dear All
I'm trying to use the gromacs version of QM/MM with DFTB3
made available here
http://cbp.cfn.kit.edu/joomla/index.php/downloads/18-gromacs-with-qm-mm-using-dftb3
by the group of  Tomas Kubar.

I was able to compile the code, however when I try to run the qm/mm
tutorial files I get this error:


Too many PME neighbors found for QM atom 1
Until now I was unable to understand the reasons of this error.
Can anybody help me?

thanks

Jacopo
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Re: [gmx-users] on editconf

[Justin Lemkul]

On 5/9/16 9:41 AM, Brett wrote:

Dear All,


When I process the md based on the on-line lysozyme tutorial, in the gmx editconf step, it writes 
"No velocities found". Will you please tell me why it writes "No velocities 
found" and what its effect? How can we have the velocities input and displayed in the editconf 
step?



editconf reads coordinate files, which generally don't have velocities.  So if 
there are no input velocities, there aren't going to magically be any in the 
output.  The .gro format can store velocities but does not have to.


-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] on editconf

[Brett]

Dear All,


When I process the md based on the on-line lysozyme tutorial, in the gmx 
editconf step, it writes "No velocities found". Will you please tell me why it 
writes "No velocities found" and what its effect? How can we have the 
velocities input and displayed in the editconf step?


Brett
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Re: [gmx-users] force calculation

[Justin Lemkul]

On 5/9/16 7:24 AM, mahdiyeh poorsargol wrote:

Dear gromacs user,
Does anyone know how to calculate the force exerted on the particle in the
simulated system from the output files?
I simulated  a system including two parallel surfactant-covered graphene
sheets, separated with the inter-sheet distance of 34.0 Å. I want to
compute the force average which need to hold them at the current location
or force exerted on a graphene sheet.
Can anyone suggest a method?


Forces are saved in the .trr and extracted with gmx traj.  If you didn't save 
forces (nstfout > 0) then use mdrun -rerun on whatever existing trajectory you 
have with a new .tpr specifying the desired output.


-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] Fixing the center of mass

[Justin Lemkul]

On 5/9/16 6:05 AM, Alexander Alexander wrote:

Dear Gromacs user,

I was wondering how the center of mass of JUST peptide can be fixd in a
system that contains a peptide, water and solid surface?



Either (1) create a virtual site that coincides with the COM of the peptide and 
use normal position restraints or (2) apply flat-bottom restraints to a central 
residue/selection or again, a virtual site.


-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] TPO and SEP is is added in residue.date

[Justin Lemkul]

On 5/9/16 12:46 AM, Mehreen Jan wrote:

respected sir!
thank you for your response!

version 5.0.7
forcefield 43a1p
Question 1
i run  phosphorylated simulation 10ns result are good known i want to extend my 
simulation to 20ns the problem is at 11ns i generate PDB i am shocked to see 
that my TPO and SEP is no more in the pdb. structure is breakdown :( i have no 
idea what happen to my pdb :( :(
1) have added these residues to residuetypes.dat
i am  saving "Protein" when selecting output from trjconv. because it it is 
protein domain



command to extend:

convert-tpr -s  md_0_1.tpr -extend 1000 -o next1.tpr

mdrun -s next1.tpr -cpi md_0_1.cpt

to combine xtc command:
trjcat -f md_0_1.xtc next1.xtc next2.xtc -o concat.xtc -cat

to generate PDB:
trjconv -s md_0_1.tpr -f md_0_1.xtc -o time_11000ps.pdb -dump 11000

and when i open PDB TPO and SEP is disappear from PDB and structure is break 
down.



If your residuetypes.dat did not contain SEP and TPO as Protein when you created 
your .tpr file, and in the even that you only chose Protein to be saved in your 
.xtc file, those coordinates are never written and you'll have to start the 
simulation over if you want them to be present.  Adding SEP and TPO to 
residuetypes.dat only when trying to execute trjconv will not help in this case. 
 I'm guessing a bit because you haven't provided your .mdp files, but this is 
the most likely case.  You can use gmx check to verify the contents of the .xtc 
files - the number of atoms will tell you whether or not you're saving 
everything you think you did.


-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] calculate electrostatic force

[masoud keramati]

Hi to all,

i have two peptides that bind together,
how i can calculate the electrostatic forces between these peptide atoms?

tnx :)
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[gmx-users] force calculation

[mahdiyeh poorsargol]

Dear gromacs user,
Does anyone know how to calculate the force exerted on the particle in the
simulated system from the output files?
I simulated  a system including two parallel surfactant-covered graphene
sheets, separated with the inter-sheet distance of 34.0 Å. I want to
compute the force average which need to hold them at the current location
or force exerted on a graphene sheet.
Can anyone suggest a method?
Thank You in advance
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[gmx-users] Analysis of protein protein interaction

[James Starlight]

Dear Gromacs users!

I am in charge with the analysis of protein-protein assosiation during
several independent md sims calculated for the same system. I would
like interesting to calculate
1* contact maps to get insight about residues important for the assosiation

2* electrostatic surface- as the dynamical property of the receptor
system - to understand whether any differences in it - seen on
different trajectories which helps me make conclusions regarding
importance of the electrostatic forces in my system in general.

Thanks so much for any help with the realization of those steps as
well as for any extra advises!

James
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Re: [gmx-users] LINCS WARRING PROBLEM

[Mark Abraham]

Hi,

Did you check out the link mdrun suggested?

Mark

On Mon, 9 May 2016 10:52 Upasana Ray  wrote:

> Step 824, time 1.648 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.041039, max 2.241032 (between atoms 585 and 587)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> 582583   39.80.2015   0.1702  0.1530
> 583584   33.60.1882   0.1285  0.1230
> 583585   94.60.1746   0.1769  0.1330
> 585586   93.90.0904   0.1061  0.1000
> 585587   91.50.2102   0.3241  0.1000
>
> ---
> Program mdrun, VERSION 5.0.7
> Source code file: /usr/local/gromacs-5.0.7/src/gromacs/mdlib/constr.c,
> line: 224
>
> Fatal error:
> Too many LINCS warnings (1002)
> If you know what you are doing you can adjust the lincs warning threshold
> in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
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[gmx-users] water model

[mahdiyeh poorsargol]

Dear Erik
Thank you for your reply.
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[gmx-users] Fixing the center of mass

[Alexander Alexander]

Dear Gromacs user,

I was wondering how the center of mass of JUST peptide can be fixd in a
system that contains a peptide, water and solid surface?

Cheers,
Alex
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[gmx-users] LINCS WARRING PROBLEM

[Upasana Ray]

Step 824, time 1.648 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.041039, max 2.241032 (between atoms 585 and 587)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
582583   39.80.2015   0.1702  0.1530
583584   33.60.1882   0.1285  0.1230
583585   94.60.1746   0.1769  0.1330
585586   93.90.0904   0.1061  0.1000
585587   91.50.2102   0.3241  0.1000

---
Program mdrun, VERSION 5.0.7
Source code file: /usr/local/gromacs-5.0.7/src/gromacs/mdlib/constr.c,
line: 224

Fatal error:
Too many LINCS warnings (1002)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
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Re: [gmx-users] water model

[Erik Marklund]

Dear Mahdiyeh,

For water molecules the constraints can be solved analytically with SETTLE, so 
no need to invoke SHAKE. SETTLE is used by default so just simulate as normal 
and you will have rigid water.

Kind regards,
Erik

> On 9 May 2016, at 09:04, mahdiyeh poorsargol  wrote:
> 
> Dear all
> I am a beginner in gromacs. I want to use water in my system. I choose the
> SPC/E water model in the topol.top file by:
> 
> ; Include water topology
> #include "spce.itp"
> 
> My question is, is rigid water molecule in the SPC/E model or should use
> the SHAKE algorithm for water in order to fix the length of bonds and
> angles?
> I would be more than pleased if someone could guide me.
> Thank You in advance
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[gmx-users] water model

[mahdiyeh poorsargol]

Dear all
I am a beginner in gromacs. I want to use water in my system. I choose the
SPC/E water model in the topol.top file by:

; Include water topology
#include "spce.itp"

My question is, is rigid water molecule in the SPC/E model or should use
the SHAKE algorithm for water in order to fix the length of bonds and
angles?
I would be more than pleased if someone could guide me.
Thank You in advance
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