Re: [gmx-users] LINCS warnings at high temperature md run

[Sidong Tu]

Hi Christopher & Mark,

My simulation worked well with the parameters given by Christopher.  The sd
integrator & lincs-order was fit in this situation while md integrator
still had lincs warnings. I'll continue my runs with sd.
Thank you very much for your help!


Best wishes,
Sidong

Message: 4
> Date: Thu, 11 Aug 2016 15:51:55 +
> From: Mark Abraham 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] LINCS warnings at high temperature md run
> Message-ID:
>  mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Fundamentally, at higher temperature you have higher atomic velocities, so
> atoms move further in a step. Your simulation is only stable if you apply
> constraints, but the default settings are chosen for normal temperatures
> and thus displacements. So try the kinds of things Chris suggests.
>
> Mark
>
> On Tue, 9 Aug 2016 20:35 Christopher Neale 
> wrote:
>
> > Try adding "lincs-order =  6" to your mdp file.
> >
> > The following settings don't give me lincs warnings at 500 K, though I
> > presume that the lincs-order is the essential part.
> >
> > constraints = all-bonds
> > lincs-iter =  1
> > lincs-order =  6
> > constraint_algorithm =  lincs
> > dt = 0.002
> > integrator = sd
> > tc_grps =  System
> > tau_t   =  1.0
> > ld_seed =  -1
> >
> > failing that, post your full .mdp file.
> >
> >
> >
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sidong
> Tu
> > 
> > Sent: 09 August 2016 14:49:03
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Cc: Chandan K Choudhury
> > Subject: [gmx-users] LINCS warnings at high temperature md run
> >
> > Dear all,
> >
> > I was trying to simulate lysozyme and polymer in water model tip3p using
> > charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU
> and
> > the system size was about 60,000 atoms. I have done equilibrium with
> > Berendsen(B) and Parrinello-Rahman(PR), and then md. The thermal
> coupling I
> > used was v-rescale.
> > I always got a LINCS warning and my job stopped during the md. Here's the
> > parameter I have used:
> > Stage  Position_Constraint  Pcoupl  gen_vel  LINCS   dt
> > nsteps
> > 1 Protein & polymerB   yes all bonds0.002
> > 200,000
> > 2 ProteinB   yes all bonds
> > 0.002200,000
> > 3 None   B   yes all bonds
> > 0.002200,000
> > 4 None   PR no   all bonds
> > 0.00250,000
> > 5 None   PR no   h bonds
> > 0.0021.25e+8
> >
> > At stage 5, the md run stopped at 149 steps and showed relative
> constraint
> > deviation after LINCS.
> >
> > I have searched for this warning and there is an explanation that it
> might
> > be introduced by the bad equilibrium. Then I added a equilibrium stage
> with
> > Berendsen pressure coupling after stage 3 with LINCS constraints of h
> bonds
> > for 50,000 steps without position constraints.
> >
> > This time there was still warings with LINCS and it stopped at step 79026
> > in md:
> >
> > Step 79026, time 158.052 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms 15.598468, max 1553.834961 (between atoms 15966 and 15968)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >   15941  15943   40.70.2082   0.1109  0.
> >   15945  15946   75.60.2551   7.7014  0.
> >   15945  15947   90.00.2299   4.2042  0.
> >   15949  15950   67.80.1543   0.1150  0.
> >   15949  15951   86.20.1658   8.9758  0.
> >   15966  15967   90.00.   0.2587  0.
> >   15966  15968  143.10. 172.7422  0.
> >   15970  15971   90.00.   0.1405  0.
> > Wrote pdb files with previous and current coordinates
> >
> > The simulation worked well with dt=0.001 without LINCS. But I still want
> to
> > find if there is a way to simulate at high temperature(500K) with
> dt=0.002
> > so that I can use less steps?
> >
> >
> > --
> > Sidong Tu
> > Department of Materials Science and Engineering
> > Clemson University
> > Phone: (213)265-6768
> > --
> > 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
> >
> > * 

Re: [gmx-users] mdrun on GPU

[Mark Abraham]

Hi,

Please get a non-PLUMED version working first. When you report a command
line, please copy and paste it, rather than type it out and make typos.
Probably you are running a version of GROMACS that was compiled to run on a
different kind of node, but you need to find out what kinds of nodes your
cluster has in it to evaluate that guess.

Mark

On Fri, Aug 12, 2016 at 4:54 PM susanta haldar 
wrote:

> hi users,
>
> I am trying to run a simulation in a 16 core node having 2 GPUs build
> inside and I am using the following command --
>
> gmx_omp_mpi_gpu mdrun -ntmpi 2 -ntopm 8 -s *.tpr ...
>
> and I am getting the following error-
>  q/var/spool/sge/default/p01/job_scripts/5226: line 30: 25864 Illegal
> instruction (core dumped) ${GMXBIN}/gmx_omp_mpi_gpu mdrun -ntmpi
> ${NUM_GPUS} -ntomp ${OMP_NUM_THREADS} -s topol.tpr -deffnm LEMU04-funnel
> -plumed plumed.dat
>
> any suggestion is appreciated.
>
> thanks in advance.
>
>
> --
> Susanta Haldar
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic.
> --
> 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/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.

Re: [gmx-users] Creating topology for Cu-containing enzyme,

[João M . Damas]

Hi Francesca,

Please contact me directly.

Best,
João

On Fri, Aug 12, 2016 at 8:23 AM, Francesca Lønstad Bleken <
francescal.ble...@sintef.no> wrote:

> Hi,
>
> Thank you Joao, Justin and Marlon for your answers.
>
> Joao, I have been looking at your article the last days as it explains
> very well what you have done, particularly in the Supplementary info, so
> I am very happy that you answered this thread. Would it be possible for me
> to look at your specbond.dat, .rtp and .itp files so that I better can
> ensure that I am doing things the right way?
> Your system is very similar to mine, so I think I would learn a lot from
> looking at your setup. I hope this is not an inappropriate request, I will
> of course acknowledge you help if this work comes to a publication.
>
> Best regards,
> Francesca
>
>
>
> Date: Thu, 11 Aug 2016 15:40:30 +0100
>
> From: Jo?o M. Damas >
>
> To: Discussion list for GROMACS users >
>
> Subject: Re: [gmx-users] Creating topology for Cu-containing enzyme,
>
> GROMOS96 force field.
>
> Message-ID:
>
> 

[gmx-users] mdrun on GPU

[susanta haldar]

hi users,

I am trying to run a simulation in a 16 core node having 2 GPUs build
inside and I am using the following command --

gmx_omp_mpi_gpu mdrun -ntmpi 2 -ntopm 8 -s *.tpr ...

and I am getting the following error-
 q/var/spool/sge/default/p01/job_scripts/5226: line 30: 25864 Illegal
instruction (core dumped) ${GMXBIN}/gmx_omp_mpi_gpu mdrun -ntmpi
${NUM_GPUS} -ntomp ${OMP_NUM_THREADS} -s topol.tpr -deffnm LEMU04-funnel
-plumed plumed.dat

any suggestion is appreciated.

thanks in advance.


-- 
Susanta Haldar
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic.
-- 
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.

Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

[Andreas Mecklenfeld]

Dear Mark and Justin,

I've switched to function type 1 and the simulation runs. I thought the 
function type would correspond to the type of the comb-rule and missed 
the information given in the 5.8.1 section of the manual.


Thanks a lot!

Andreas


Am 12.08.2016 um 14:15 schrieb Justin Lemkul:



On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote:

Hello Mark,

sorry for the confusion I've created. My system refers to a solute in 
water
(which has only LJ-parameters for the oxygen atom). Within the 
solute, there are

two approaches to deal with LJ-interactions:

1) intramolecular interactions (including 1-4 and far-off interactions)
2) intermolecular interactions with the oxygens of ambient water

There are certain atom types, which handle points 1) and 2) with 
different sets
of LJ-parameters. Since the water oxygen is not included within the 
solute
topology, the pair potential between the affected solute atomtype and 
the

water-oxygen atomtype therefore has to be intermolecular.

My .top file looks like this:

# 




[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 o3   o3  0.0  0.0   A 2.95992e-01 
8.78640e-01 ; 1.66

0.2100
 oa   oa  0.0  0.0   A 3.06647e-01 
8.80314e-01 ; 1.72

0.2104
 od   od  0.0  0.0   A 2.95992e-01 
8.78640e-01 ; 1.66

0.2100
 nd   nd  0.0  0.0   A 3.25000e-01 
7.11280e-01 ; 1.82

0.1700
 nl   nl  0.0  0.0   A 3.25000e-01 
7.11280e-01 ; 1.82

0.1700
 sh   sh  0.0  0.0   A 3.56359e-01 
1.04600e+00 ; 2.00

0.2500
 o3i  o3i 0.0  0.0   A 0.331503 0.878640; 
1.66  0.2100
 oai  oai 0.0  0.0   A 0.295778 0.880314; 
1.72  0.2104
 odi  odi 0.0  0.0   A 0.320724 0.878640; 
1.66  0.2100
 ndi  ndi 0.0  0.0   A 0.349232 0.711280; 
1.82  0.1700
 nli  nli 0.0  0.0   A 0.299003 0.711280; 
1.82  0.1700
 shi  shi 0.0  0.0   A 0.334978 1.046000; 
2.00  0.2500
 c3   c3  0.0  0.0   A 3.39967e-01 
4.57730e-01 ; 1.91

0.1094
 hc   hc  0.0  0.0   A 2.64953e-01 
6.56888e-02 ; 1.49

0.0157
 cc   0.0  0.0   A 3.39967e-01 
3.59824e-01 ; 1.91

0.0860
 oo   0.0  0.0   A 2.95992e-01 
8.78640e-01 ; 1.66

0.2100
 nn   0.0  0.0   A 3.25000e-01 
7.11280e-01 ; 1.82

0.1700
 hn   hn  0.0  0.0   A 1.06908e-01 
6.56888e-02 ; 0.60

0.0157
 cc   cc  0.0  0.0   A 3.39967e-01 
3.59824e-01 ; 1.91

0.0860
 cd   cd  0.0  0.0   A 3.39967e-01 
3.59824e-01 ; 1.91

0.0860
 h4   h4  0.0  0.0   A 2.51055e-01 
6.27600e-02 ; 1.41

0.0150
 h5   h5  0.0  0.0   A 2.42146e-01 
6.27600e-02 ; 1.36

0.0150
 na   na  0.0  0.0   A 3.25000e-01 
7.11280e-01 ; 1.82

0.1700
 h1   h1  0.0  0.0   A 2.47135e-01 
6.56888e-02 ; 1.39

0.0157
 ss   ss  0.0  0.0   A 3.56359e-01 
1.04600e+00 ; 2.00

0.2500
 ca   ca  0.0  0.0   A 3.39967e-01 
3.59824e-01 ; 1.91

0.0860
 ha   ha  0.0  0.0   A 2.59964e-01 
6.27600e-02 ; 1.46

0.0150
 oh   oh  0.0  0.0   A 3.06647e-01 
8.80314e-01 ; 1.72

0.2104
 ho   ho  0.0  0.0   A 0.0e+00 
0.0e+00 ; 0.00

0.
HW_tip4pew   1   1.008   0.  A   0.0e+00 0.0e+00
OW_tip4pew   8  16.000.  A   3.16435e-01 6.80946e-01
MW   0   0.  0.  D   0.0e+00 0.0e+00

[ nonbond_params ]
OW_tip4pewo3i2 0.3239690.773503
OW_tip4pewoai2 0.3061070.774239
OW_tip4pewodi2 0.3185790.773503
OW_tip4pewndi2 0.3328340.695948
OW_tip4pewnli2 0.3077190.695948
OW_tip4pewshi2 0.3257060.843961



#include "Asn.itp"
#include "tip4pew.itp"



 [ system ]
Asn in tip4pew


 [ molecules ]
; molecule namenr.
Asn1
SOL900



# 




When I comment out the [ non_bond_params ] section, everything works 
fine, thus

I would locate the error to this point.
The error I receive is actually the one from the mail subject:

ERROR 1 [file topol.top, line 44]:
  Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

followed by repetitions regarding the other lines in the [ 
non_bond_params ]

section.



You have 

[gmx-users] upcoming GROMACS-related events

[Mark Abraham]

Hi GROMACS people!

You may be interested in some upcoming events related to GROMACS, both to
use and to develop code around. These come to you courtesy of the EU-funded
HPC Center of Excellence called BioExcel (http://bioexcel.eu/). We may also
have some other events next year, perhaps associated with the PRACE Spring
School in Stockholm, or later in Gottingen.

Details follow:

*4th Sept. 2016 - BioExcel 1st Annual Meeting: “Advanced Simulations for
Biomolecular Research” SIG @ ECCB 2016*

*Location:* The Hague, Netherlands

*Application deadline: *Friday 19th August 2016

Description: SIG BioExcel is a major venue for knowledge exchange and
networking for the computational biomolecular research community. It brings
together stakeholders of 1) core applications that are supported by the
center – HADDOCK (integrative modelling), GROMACS (molecular dynamics
simulations) and CPMD (hybrid QM/MM methods) and 2) workflow environments
and platforms for data integration and analysis such as Galaxy, Taverna,
Open PHACTS, COMPSs and Copernicus.

*Registration via www.eccb2016.org    *



*17-19th Oct. 2016 - GROMACS hackathon 2016*

*Location:* Barcelona, Spain

*Application deadline: *n/a

*Description:* Get together with core GROMACS developers from around the
world to hack together on code! Bring your own laptop and coding problem –
new integrator, fancy free-energy method, cool analysis tool, automated
parameterizer, workflow implementation, meta-dynamics driver, tricky bug to
fix, API design question, etc. Be ready to ask and answer questions with
the gurus, and come away with new code running, progressed or well planned!

*Full details and registration via bioexcel.eu/events
*



*20-21st Oct. 2016 - BioExcel: workflow training for computational
biomolecular research*

*Location:* Barcelona, Spain

*Application deadline:* Friday 9th September 2016

*Description:* The purpose of this workshop is to (1) provide an overview
of the most commonly used workflow managers in the computational
biomolecular field, both in a theoretical and practical way, with hands-on
practice sessions. (2) Find out about how BioExcel – Europe’s new Centre of
Excellence for Computational BioMolecular Research – will help you to
develop and run your own pipelines using these tools and introduce you to
the BioExcel Workflows Interest Group. (3) Together with experts on the
different workflow managers, identify the best approach for your particular
workflow problem in a “Bring Your Own Workflow” session

*Full details and registration via bioexcel.eu/events
*

Happy simulating!

Mark Abraham
GROMACS development manager
-- 
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.

Re: [gmx-users] job suspended in local workstation

[Albert]

there is no any errors messages if I run it from terminal for a specific 
step Everything goes well





On 08/12/2016 03:46 PM, Mark Abraham wrote:

Hi,

Run job.whateveritis and see the error message.

Mark


--
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.

Re: [gmx-users] job suspended in local workstation

[Mark Abraham]

Hi,

Run job.whateveritis and see the error message.

Mark

On Fri, Aug 12, 2016 at 3:33 PM Albert  wrote:

> Hello:
>
> I wrote all steps for Gromacs MD simulation in a .tcsh script. Then I
> submitted the job into the local GPU workstation by command line:
>
> nohup  ./job.tcsh &
>
> However, I obtained the following messages immediately:
>
> nohup ./job.csh &
> [1] 13433
>
>
> No any steps is running after I submit the job.
>
> I am just wondering how to solve the problem?
>
> Thanks a lot
>
>
>
> --
> 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/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.

[gmx-users] job suspended in local workstation

[Albert]

Hello:

I wrote all steps for Gromacs MD simulation in a .tcsh script. Then I 
submitted the job into the local GPU workstation by command line:


nohup  ./job.tcsh &

However, I obtained the following messages immediately:

nohup ./job.csh &
[1] 13433


No any steps is running after I submit the job.

I am just wondering how to solve the problem?

Thanks a lot



--
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.

[gmx-users] Energy minimization, of peptide-ligand, tearing peptide apart

[Richard Kerr]

Hi everyone

I am currently trying to perform a peptide-ligand (~4000 and 110 Da
respectively) simulated annealing study using gromacs (5.1.2) with Amber
force fields.  Under the initial energy minimization step (minim.mdp and
nvt.mdp) I am finding that the step fails.  It then kicks out pdb files,
which when opened depicts a ligand that has 'exploded' with the peptide
fragmented into a number of pieces.

Under the same conditions, I can get the peptide to run with a ligand about
twice the size of the above, which follows through to completion of all
annealing steps to gain output pdb files.  Accounting for a peptide only
system, the peptide will also follow through to completion.

Is anyone able to suggest how to optimize the minim/nvt files, or make
sense of the log file.

I have linked to the minim, nvt and output log files below.
minim
https://www.dropbox.com/s/80wwe8n2ncpg77t/minim.mdp?dl=0

nvt
https://www.dropbox.com/s/qruyanl8vg1a3no/nvt.mdp?dl=0

Log details (md_temp.e20786725)
https://www.dropbox.com/s/0fnjm05ub85yiun/md_temp_e20786725.txt?dl=0

Any help would be greatly appreciated.

Richard
-- 
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.

[gmx-users] semiisotropic pcoupltype in PMF pull

[Alexander Alexander]

Dear gromacs user,

In my normal MD simulation of adsorption of a short peptide into a solid
surface in water solution, my system is nicely equilibrating (after 1.5 ns
NPT using isotropic condition) to an average around 1 bar pressure which is
my desire.

However, in my PMF calculations in which I try to pull away peptide from
solid surface in the Z direction, first of all, the PBC problem forced me
to use the "direction-periodic" instead of "direction" and then
"semiisotropic" with zero compressibility in the Z direction instead of
"isotropic". Below is my pull keywords. These changes respect to my normal
MD causes not to reach to equilibration of 1 bar pressure after 1.5 ns, in
each window, but the pressure average  is around -500 like below in one
window

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -591.2371.7 255.97   -8.49498  (bar)

or in another window is would be like:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure127.992   0.97199.158   -4.91034  (bar)

Another window:

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   -273.501   0.34201.917   0.521768  (bar)


Would you please let me know if the pressures are fine or I should increase
the time of NPT equilibration more than 1.5 ns?


pcoupl   = berendsen
Pcoupltype   = semiisotropic   ;*
tau_p = 2.5
compressibility  = 4.46e-5  0.0;*
ref_p   = 1.0  1.0
refcoord-scaling= com

pull   = yes
pull-ngroups= 2
pull-ncoords = 1
pull-group1-name= Protein
pull-group2-name= Slab

pull-coord1-groups   = 1 2
pull-coord1-type= umbrella
pull-coord1-dim = N N Y
pull-coord1-init  = WINDOW
pull-coord1-start= no
pull-coord1-rate = 0.0
pull-coord1-vec  = 0.0 0.0 1.0   ;*
pull-coord1-geometry= direction-periodic   ;*
pull-coord1-k  = 5000
pull-print-components= Yes

Also, If the my entries for the pull code are fine? any suggestion in this
system, please?

Thanks in advance.

Regards.
Alex
-- 
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.

Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

[Justin Lemkul]

On 8/12/16 8:11 AM, Andreas Mecklenfeld wrote:

Hello Mark,

sorry for the confusion I've created. My system refers to a solute in water
(which has only LJ-parameters for the oxygen atom). Within the solute, there are
two approaches to deal with LJ-interactions:

1) intramolecular interactions (including 1-4 and far-off interactions)
2) intermolecular interactions with the oxygens of ambient water

There are certain atom types, which handle points 1) and 2) with different sets
of LJ-parameters. Since the water oxygen is not included within the solute
topology, the pair potential between the affected solute atomtype and the
water-oxygen atomtype therefore has to be intermolecular.

My .top file looks like this:

#


[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 o3   o3  0.0  0.0   A 2.95992e-01 8.78640e-01 ; 1.66
0.2100
 oa   oa  0.0  0.0   A 3.06647e-01 8.80314e-01 ; 1.72
0.2104
 od   od  0.0  0.0   A 2.95992e-01 8.78640e-01 ; 1.66
0.2100
 nd   nd  0.0  0.0   A 3.25000e-01 7.11280e-01 ; 1.82
0.1700
 nl   nl  0.0  0.0   A 3.25000e-01 7.11280e-01 ; 1.82
0.1700
 sh   sh  0.0  0.0   A 3.56359e-01 1.04600e+00 ; 2.00
0.2500
 o3i  o3i 0.0  0.0   A 0.331503 0.878640; 1.66  
0.2100
 oai  oai 0.0  0.0   A 0.295778 0.880314; 1.72  
0.2104
 odi  odi 0.0  0.0   A 0.320724 0.878640; 1.66  
0.2100
 ndi  ndi 0.0  0.0   A 0.349232 0.711280; 1.82  
0.1700
 nli  nli 0.0  0.0   A 0.299003 0.711280; 1.82  
0.1700
 shi  shi 0.0  0.0   A 0.334978 1.046000; 2.00  
0.2500
 c3   c3  0.0  0.0   A 3.39967e-01 4.57730e-01 ; 1.91
0.1094
 hc   hc  0.0  0.0   A 2.64953e-01 6.56888e-02 ; 1.49
0.0157
 cc   0.0  0.0   A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
 oo   0.0  0.0   A 2.95992e-01 8.78640e-01 ; 1.66
0.2100
 nn   0.0  0.0   A 3.25000e-01 7.11280e-01 ; 1.82
0.1700
 hn   hn  0.0  0.0   A 1.06908e-01 6.56888e-02 ; 0.60
0.0157
 cc   cc  0.0  0.0   A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
 cd   cd  0.0  0.0   A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
 h4   h4  0.0  0.0   A 2.51055e-01 6.27600e-02 ; 1.41
0.0150
 h5   h5  0.0  0.0   A 2.42146e-01 6.27600e-02 ; 1.36
0.0150
 na   na  0.0  0.0   A 3.25000e-01 7.11280e-01 ; 1.82
0.1700
 h1   h1  0.0  0.0   A 2.47135e-01 6.56888e-02 ; 1.39
0.0157
 ss   ss  0.0  0.0   A 3.56359e-01 1.04600e+00 ; 2.00
0.2500
 ca   ca  0.0  0.0   A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
 ha   ha  0.0  0.0   A 2.59964e-01 6.27600e-02 ; 1.46
0.0150
 oh   oh  0.0  0.0   A 3.06647e-01 8.80314e-01 ; 1.72
0.2104
 ho   ho  0.0  0.0   A 0.0e+00 0.0e+00 ; 0.00
0.
HW_tip4pew   1   1.008   0.  A   0.0e+00  0.0e+00
OW_tip4pew   8  16.000.  A   3.16435e-01  6.80946e-01
MW   0   0.  0.  D   0.0e+00  0.0e+00

[ nonbond_params ]
OW_tip4pewo3i2 0.3239690.773503
OW_tip4pewoai2 0.3061070.774239
OW_tip4pewodi2 0.3185790.773503
OW_tip4pewndi2 0.3328340.695948
OW_tip4pewnli2 0.3077190.695948
OW_tip4pewshi2 0.3257060.843961



#include "Asn.itp"
#include "tip4pew.itp"



 [ system ]
Asn in tip4pew


 [ molecules ]
; molecule namenr.
Asn1
SOL900



#


When I comment out the [ non_bond_params ] section, everything works fine, thus
I would locate the error to this point.
The error I receive is actually the one from the mail subject:

ERROR 1 [file topol.top, line 44]:
  Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

followed by repetitions regarding the other lines in the [ non_bond_params ]
section.



You have specified type 2 for the [ nonbond_params ] section, which corresponds 
to Buckingham.  If you want normal LJ, set the type field to 1.


-Justin




Thanks for your help!
Andreas





Am 12.08.2016 um 09:49 schrieb Mark Abraham:

Hi,

On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld <
a.mecklenf...@tu-braunschweig.de> wrote:


Hello Mark,

thanks for the 

Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

[Andreas Mecklenfeld]

Hello Mark,

sorry for the confusion I've created. My system refers to a solute in 
water (which has only LJ-parameters for the oxygen atom). Within the 
solute, there are two approaches to deal with LJ-interactions:


1) intramolecular interactions (including 1-4 and far-off interactions)
2) intermolecular interactions with the oxygens of ambient water

There are certain atom types, which handle points 1) and 2) with 
different sets of LJ-parameters. Since the water oxygen is not included 
within the solute topology, the pair potential between the affected 
solute atomtype and the water-oxygen atomtype therefore has to be 
intermolecular.


My .top file looks like this:

#

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ atomtypes ]
;name   bond_type mass charge   ptype   sigma epsilon   Amb
 o3   o3  0.0  0.0   A 2.95992e-01 8.78640e-01 
; 1.66  0.2100
 oa   oa  0.0  0.0   A 3.06647e-01 8.80314e-01 
; 1.72  0.2104
 od   od  0.0  0.0   A 2.95992e-01 8.78640e-01 
; 1.66  0.2100
 nd   nd  0.0  0.0   A 3.25000e-01 7.11280e-01 
; 1.82  0.1700
 nl   nl  0.0  0.0   A 3.25000e-01 7.11280e-01 
; 1.82  0.1700
 sh   sh  0.0  0.0   A 3.56359e-01 1.04600e+00 
; 2.00  0.2500
 o3i  o3i 0.0  0.0   A 0.331503 0.878640; 
1.66  0.2100
 oai  oai 0.0  0.0   A 0.295778 0.880314; 
1.72  0.2104
 odi  odi 0.0  0.0   A 0.320724 0.878640; 
1.66  0.2100
 ndi  ndi 0.0  0.0   A 0.349232 0.711280; 
1.82  0.1700
 nli  nli 0.0  0.0   A 0.299003 0.711280; 
1.82  0.1700
 shi  shi 0.0  0.0   A 0.334978 1.046000; 
2.00  0.2500
 c3   c3  0.0  0.0   A 3.39967e-01 4.57730e-01 
; 1.91  0.1094
 hc   hc  0.0  0.0   A 2.64953e-01 6.56888e-02 
; 1.49  0.0157
 cc   0.0  0.0   A 3.39967e-01 3.59824e-01 
; 1.91  0.0860
 oo   0.0  0.0   A 2.95992e-01 8.78640e-01 
; 1.66  0.2100
 nn   0.0  0.0   A 3.25000e-01 7.11280e-01 
; 1.82  0.1700
 hn   hn  0.0  0.0   A 1.06908e-01 6.56888e-02 
; 0.60  0.0157
 cc   cc  0.0  0.0   A 3.39967e-01 3.59824e-01 
; 1.91  0.0860
 cd   cd  0.0  0.0   A 3.39967e-01 3.59824e-01 
; 1.91  0.0860
 h4   h4  0.0  0.0   A 2.51055e-01 6.27600e-02 
; 1.41  0.0150
 h5   h5  0.0  0.0   A 2.42146e-01 6.27600e-02 
; 1.36  0.0150
 na   na  0.0  0.0   A 3.25000e-01 7.11280e-01 
; 1.82  0.1700
 h1   h1  0.0  0.0   A 2.47135e-01 6.56888e-02 
; 1.39  0.0157
 ss   ss  0.0  0.0   A 3.56359e-01 1.04600e+00 
; 2.00  0.2500
 ca   ca  0.0  0.0   A 3.39967e-01 3.59824e-01 
; 1.91  0.0860
 ha   ha  0.0  0.0   A 2.59964e-01 6.27600e-02 
; 1.46  0.0150
 oh   oh  0.0  0.0   A 3.06647e-01 8.80314e-01 
; 1.72  0.2104
 ho   ho  0.0  0.0   A 0.0e+00 0.0e+00 
; 0.00  0.

HW_tip4pew   1   1.008   0.  A   0.0e+00  0.0e+00
OW_tip4pew   8  16.000.  A   3.16435e-01  6.80946e-01
MW   0   0.  0.  D   0.0e+00  0.0e+00

[ nonbond_params ]
OW_tip4pewo3i2 0.3239690.773503
OW_tip4pewoai2 0.3061070.774239
OW_tip4pewodi2 0.3185790.773503
OW_tip4pewndi2 0.3328340.695948
OW_tip4pewnli2 0.3077190.695948
OW_tip4pewshi2 0.3257060.843961



#include "Asn.itp"
#include "tip4pew.itp"



 [ system ]
Asn in tip4pew


 [ molecules ]
; molecule namenr.
Asn1
SOL900



#

When I comment out the [ non_bond_params ] section, everything works 
fine, thus I would locate the error to this point.

The error I receive is actually the one from the mail subject:

ERROR 1 [file topol.top, line 44]:
  Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

followed by repetitions regarding the other lines in the [ 
non_bond_params ] section.




Thanks for your help!
Andreas





Am 12.08.2016 um 09:49 schrieb Mark Abraham:

Hi,

On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld <
a.mecklenf...@tu-braunschweig.de> wrote:


Hello Mark,

thanks for the reply. The point is, I don't.


Ah, I read your original email more closely now. The use of a subject line
that reflected your error message rather than 

[gmx-users] topology doubt.

[kalai sivam]

 dear  All gromacs user,
 i have finished all steps  for preparing topology.


my doubt is, after simulation is any possible to show the error or
structural modification???
 or warning error..
 pls say suggestion...any one.
-- 
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.

Re: [gmx-users] Creating topology for Cu-containing enzyme, GROMOS96 force field.

[Mark Abraham]

Hi,

On Wed, Aug 10, 2016 at 9:27 PM Francesca Lønstad Bleken <
francescal.ble...@sintef.no> wrote:

> I am interested in a metalloenzyme with Cu and I have found several
> studies in the literature on systems similar to mine using GROMACS and the
> Gromos force field. I see that GROMOS contains parameters for Cu, and I
> intend to keep the Cu-protein distances for the ligand atoms fixated during
> MD (as I see most of the previous papers have done). However, I do not
> understand how to prepare the topology for the cofactors with Cu, and none
> of the papers discuss this.


Note for future - if a paper doesn't provide enough details for you to
consider reproducing the work, then you should contact the corresponding
author and ask for them. Reputable people will be happy to share more
details, and often even their topology files. If you get no satisfaction,
then (eventually) the editor will retract the paper...

Mark


> pdb2gmx does not recognize it and the PRODRG server suggested in the
> excellent tutorial on protein-ligand system does not recognize Cu.
> Do you have a suggestion for how to proceed with creating the topology
> including Cu (in one case) and Cu-containing (another case) co-factors?
> Direction towards tutorials that I might have missed are also appreciated.
>
> Kind regards,
> Francesca
> --
> 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/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.

Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

[Mark Abraham]

Hi,

On Fri, Aug 12, 2016 at 9:16 AM Andreas Mecklenfeld <
a.mecklenf...@tu-braunschweig.de> wrote:

> Hello Mark,
>
> thanks for the reply. The point is, I don't.


Ah, I read your original email more closely now. The use of a subject line
that reflected your error message rather than your intention confused me.


> I found some Lennard-Jones
> parametrization in literature that distinguishes between intra- and
> intermolecular (oxygen atom of water) interactions.


Um, typical water models have no intra-molecular LJ interactions.


> My intention was
> thus to define the specific eps_ij and sigma_ij for the corresponding
> atomtypes, which I thought should be dealt with in the [ nonbond_params
> ] section. All parameters are for Lennard-Jones and this is the
> potential I want to use. I have no idea why the usage of Buckingham is
> assumed. I'm using Gromacs 5.1 btw.
>

Then somewhere (e.g. [nonbond_params]) you are using a number that is being
interpreted as a function type that is Buckingham, which of course makes no
sense for a code that assumes each atom type has at most one set of LJ
parameters. But we haven't seen your full topology or full error message.

Mark


> Thanks,
> Andreas
>
>
>
> Am 11.08.2016 um 17:59 schrieb Mark Abraham:
> > Hi,
> >
> > How do you want your atoms with lj parameters to interact with atoms with
> > Buckingham parameters?
> >
> > Mark
> >
> > On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld <
> > a.mecklenf...@tu-braunschweig.de> wrote:
> >
> >> Dear Gromacs-users,
> >>
> >> I'm trying to modify some intermolecular Lennard-Jones interactions
> >> based on the GAFF force field. I've altered the topology file according
> to
> >>
> >>
> >>
> 
> >>
> >> [ defaults ]
> >> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
> >> 1   2   yes 0.5 0.8333
> >>
> >> [ atomtypes ]
> >> ...
> >>
> >> [ nonbond_params ]
> >> type1type2sigmaepsilon
> >> ...
> >>
> >> #include ...
> >>
> >>[ system ]
> >> ...
> >>
> >>[ molecules ]
> >> ...
> >>
> >>
> >>
> >>
> >>
> 
> >>
> >> Sigma and epsilon for atoms type1 and type2 are calculated according to
> >> the Lorentz-Berthelot combination rule. The error I receive is
> >>
> >> "Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)",
> >> though I obviously want to use LJ and did not intentionally set any flag
> >> for Buckingham. Is there any way to fix this?
> >>
> >> Cheers,
> >>
> >> Andreas
> >>
> >>
> >> --
> >> M. Sc. Andreas Mecklenfeld
> >> Stipendiat
> >>
> >> Technische Universität Braunschweig
> >> Institut für Thermodynamik
> >> Hans-Sommer-Straße 5
> >> 38106 Braunschweig
> >> Deutschland / Germany
> >>
> >> Tel: +49 (0)531 391-2634
> >> Fax: +49 (0)531 391-7814
> >>
> >> http://www.ift-bs.de
> >>
> >> --
> >> 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.
>
> --
> M. Sc. Andreas Mecklenfeld
> Stipendiat
>
> Technische Universität Braunschweig
> Institut für Thermodynamik
> Hans-Sommer-Straße 5
> 38106 Braunschweig
> Deutschland / Germany
>
> Tel: +49 (0)531 391-2634
> Fax: +49 (0)531 391-7814
>
> http://www.ift-bs.de
>
> --
> 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/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.

Re: [gmx-users] Creating topology for Cu-containing enzyme,

[Francesca Lønstad Bleken]

Hi,

Thank you Joao, Justin and Marlon for your answers.

Joao, I have been looking at your article the last days as it explains very 
well what you have done, particularly in the Supplementary info, so
I am very happy that you answered this thread. Would it be possible for me to 
look at your specbond.dat, .rtp and .itp files so that I better can ensure that 
I am doing things the right way?
Your system is very similar to mine, so I think I would learn a lot from 
looking at your setup. I hope this is not an inappropriate request, I will of 
course acknowledge you help if this work comes to a publication.

Best regards,
Francesca



Date: Thu, 11 Aug 2016 15:40:30 +0100

From: Jo?o M. Damas >

To: Discussion list for GROMACS users 
>

Subject: Re: [gmx-users] Creating topology for Cu-containing enzyme,

GROMOS96 force field.

Message-ID:

Re: [gmx-users] Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)

[Andreas Mecklenfeld]

Hello Mark,

thanks for the reply. The point is, I don't. I found some Lennard-Jones 
parametrization in literature that distinguishes between intra- and 
intermolecular (oxygen atom of water) interactions. My intention was 
thus to define the specific eps_ij and sigma_ij for the corresponding 
atomtypes, which I thought should be dealt with in the [ nonbond_params 
] section. All parameters are for Lennard-Jones and this is the 
potential I want to use. I have no idea why the usage of Buckingham is 
assumed. I'm using Gromacs 5.1 btw.


Thanks,
Andreas



Am 11.08.2016 um 17:59 schrieb Mark Abraham:

Hi,

How do you want your atoms with lj parameters to interact with atoms with
Buckingham parameters?

Mark

On Fri, 5 Aug 2016 08:53 Andreas Mecklenfeld <
a.mecklenf...@tu-braunschweig.de> wrote:


Dear Gromacs-users,

I'm trying to modify some intermolecular Lennard-Jones interactions
based on the GAFF force field. I've altered the topology file according to




[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 0.5 0.8333

[ atomtypes ]
...

[ nonbond_params ]
type1type2sigmaepsilon
...

#include ...

   [ system ]
...

   [ molecules ]
...






Sigma and epsilon for atoms type1 and type2 are calculated according to
the Lorentz-Berthelot combination rule. The error I receive is

"Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)",
though I obviously want to use LJ and did not intentionally set any flag
for Buckingham. Is there any way to fix this?

Cheers,

Andreas


--
M. Sc. Andreas Mecklenfeld
Stipendiat

Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814

http://www.ift-bs.de

--
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.


--
M. Sc. Andreas Mecklenfeld
Stipendiat

Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
Fax: +49 (0)531 391-7814

http://www.ift-bs.de

--
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.