[gmx-users] Tetrahedral order parameter

[Omkar Singh]

Hi all gmx-users,
I have a water-protein simulated  system. I  want to calculate the
Tetrahedral order parameter. Can anybody help me regarding this issue.


On Thu, Aug 1, 2019, 00:52 David van der Spoel  wrote:

> Den 2019-07-31 kl. 15:00, skrev Omkar Singh:
> > I calculated these two vectors with Z-axis  now I want to  make
> > distribution plot p(costheeta) Vs cos(theeta). How can I plot because it
> is
> > giving the value only theeta. Is there any command.
> Try write your own script.
> > Thanks
> >
> > On Wed, Jul 31, 2019, 12:00 David van der Spoel 
> > wrote:
> >
> >> Den 2019-07-31 kl. 06:12, skrev Omkar Singh:
> >>> Thanks Sir,
> >>> I did like that only, Now how can I make the distribution plot for
> these
> >>> vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command.
> >> But
> >>> results is not proper. Can you suggest me regarding this?
> >>> Thank you
> >>>
> >> How about gmx gangle -oh ?
> >>
> >>>
> >>> On Tue, Jul 30, 2019, 17:27 David van der Spoel 
> >>> wrote:
> >>>
>  Den 2019-07-30 kl. 07:55, skrev Omkar Singh:
> > Hi,
> > I did by  "gmx gangle ..." command. But I am not getting good result,
> > because I have a doubt in ndx file.  Can you help me for making  ndx
>  file.
> > How should I select the atom for vectors.
>  For OH it should be
>  1 2
>  1 3
>  4 5
>  4 6
>  7 8
>  7 9
>  etc., assuming a three particle water model with atoms O H H.
>  For HH it should be
>  2 3
>  5 6
>  8 9
>  etc.
>  A simple script would do it. The dipole vector is somewhat harder.
> > Thanks
> >
> > On Mon, Jul 29, 2019, 22:50 David van der Spoel <
> sp...@xray.bmc.uu.se>
> > wrote:
> >
> >> Den 2019-07-29 kl. 18:26, skrev Omkar Singh:
> >>> Hi,
> >>> Meaning is that If I want to calculate angle between OH, HH and dip
> >> vector
> >>> with positive Z-axis. How can I make index file for this issue? And
> >> is
>  it
> >>> possible that the angle distribution of these vectors for bulk
> water
> >>> aproximatly linear. Hope now question is clear.
> >> Probably. Check gmx gangle -g2 z
> >>>
> >>> Thanks
> >>>
> >>> On Mon, Jul 29, 2019, 16:33 David van der Spoel <
> >> sp...@xray.bmc.uu.se>
> >>> wrote:
> >>>
>  Den 2019-07-29 kl. 12:24, skrev Omkar Singh:
> > Hello everyone,
> > Is it possible that the probability distribution of HH, OH vector
> >> for
>  bulk
> > water is approximately linear?
> >
>  What do you mean?
> 
>  --
>  David van der Spoel, Ph.D., Professor of Biology
>  Head of Department, Cell & Molecular Biology, Uppsala University.
>  Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>  http://www.icm.uu.se
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> 
> >>
> >>
> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Head of Department, Cell & Molecular Biology, Uppsala University.
> >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> >> http://www.icm.uu.se
> >> --
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> >>
> 
> 
>  --
>  David van der Spoel, Ph.D., Professor of Biology
>  Head of Department, Cell & Molecular Biology, Uppsala University.
>  Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>  http://www.icm.uu.se
>  --
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> 
> >>
> >>
> >> --
> >> David van der Spoel, Ph.D., Professor of Biology
> >> Head of Department, Cell & Molecular Biology, Uppsala University.
> >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> >> 

[gmx-users] Gromacs-5.1.4 with CHARMM36 March 2019 RNA Residue Fatal Error

[Joseph,Newlyn]

Hello,


I'm running into the following error when trying to pdb2gmx my PDB file.


Program gmx pdb2gmx, VERSION 5.1.4
Source code file: 
/gpfs/apps/hpc.rhel7/Packages/Apps/Gromacs/5.1.4/Dist_514/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c,
 line: 645

Fatal error:
Residue 'C' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors?


I presume I'm naming my residues incorrectly, but upon closer inspection of the 
merged.rtp file within the forcefield, I see no section for RNA residues. I'm 
attempting to simulate an RNA that has the following as the first couple lines 
in the PDB:


REMARK  GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON OCT, 26. 
2018. JOB
REMARK  READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE
REMARK   DATE:10/27/18  0:52: 0  CREATED BY USER: apache
ATOM  1  H5T   C A   1 -29.997 -20.428   3.250  1.00  0.00   H
ATOM  2  O5'   C A   1 -30.685 -20.928   3.695  1.00  0.00   O
ATOM  3  C5'   C A   1 -30.499 -22.286   3.303  1.00  0.00   C
ATOM  4  H5'   C A   1 -30.674 -22.932   4.190  1.00  0.00   H
ATOM  5 H5''   C A   1 -29.451 -22.408   2.957  1.00  0.00   H
ATOM  6  C4'   C A   1 -31.442 -22.699   2.192  1.00  0.00   C
ATOM  7  H4'   C A   1 -31.693 -23.777   2.284  1.00  0.00   H
ATOM  8  O4'   C A   1 -32.682 -21.940   2.275  1.00  0.00   O
ATOM  9  C1'   C A   1 -33.141 -21.611   0.975  1.00  0.00   C
ATOM 10  H1'   C A   1 -34.185 -21.975   0.869  1.00  0.00   H


Any help or suggestions?


Newlyn Joseph, M.S.
M.D. Candidate, Class of 2023
University of Connecticut School of Medicine
nejos...@uchc.edu | new.josep...@gmail.com
(203) 584-6402
sent from Outlook Web App
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Re: [gmx-users] REMD

[Bratin Kumar Das]

Thanks for clarification.

On Thu, Aug 1, 2019 at 7:43 PM Justin Lemkul  wrote:

>
>
> On 7/31/19 1:44 AM, Bratin Kumar Das wrote:
> > Hi,
> >  I have some doubt regarding REMD simulation.
> >  1. In the .mdp file of each replica is it necessary to keep the
> > gen-temp constant?
> > as example: 300 k is the lowest temp of REMD simulation. Is it necessary
> to
> > keep the gen-temp=300 in each replica.
>
> No, because each subsystem needs to be equilibrated independently at the
> desired temperature.
>
> >  2. Is it necessary to provide -replex flag during the equilbration
> > phase of REMD simulation
>
> No, because these simulations are independent of one another. Only
> during the actual REMD do you need -replex.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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Re: [gmx-users] How to deal with "non-zero total charge" problem in gromacs?

[Dallas Warren]

Well there's your problem!  Don't ignore things like this, the software is
giving you the warning for a reason.

You are going to have to go through that process again, and fix the
starting coordinate file you are using, or the processing, depending on
which atoms are the ones missing. The residue database of the forcefield
being used to generate the topology expects each residue to have particular
atoms and atom names for each residue. If some of those are missing, then
you need to address that fact.

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#warning-atom-x-is-missing-in-residue-xxx-y-in-the-pdb-file

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 2 Aug 2019 at 11:45, sunyeping  wrote:

> I don't know where the non-integral charges come from. But When preparing
> the gro file from the initial PDB file (a protein-DNA complex), I got a
> information saying that there are 24 atoms missing in the structure, but I
> can't tell what are these atoms. Could you tell me how to fix the atom
> missing problem? Thank you.
> --
> From:孙业平 
> Sent At:2019 Aug. 1 (Thu.) 13:18
> To:gromacs.org_gmx-users ;
> Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem
> in gromacs?
>
>
>
> --
> From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> Sent At:2019 Aug. 1 (Thu.) 12:31
> To:gromacs ; 孙业平 
> Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem
> in gromacs?
>
> Hi,
> Yes you can use the (-maxwarn) flag to overcome the error. But better
> to optimize the starting structure to reduce the excess charge of your
> system.
>
> Thank you for the replay. But I have no idea of how to optimize the
> starting structure to reduce the excess charge. Could you give me some
> hints or examples or something?
>
> Best regards
>
>
>
> On Thu, Aug 1, 2019 at 9:35 AM sunyeping  wrote:
> Dear all,
>
>  I am trying to do MD simulation with protein-DNA complex with gromacs.
> When using gmx grompp to generate the tpr file for energy minimization, I
> enconters a fatal error:
>
>  Fatal error:
>  Too many warnings (1).
>  If you are sure all warnings are harmless, use the -maxwarn option.
>
>  There are two notes and one warning arose with grompp, and they are:
>
>  NOTE 1 [file em.mdp]:
>With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>that with the Verlet scheme, nstlist has no effect on the accuracy of
>your simulation.
>  NOTE 2 [file topol.top, line 55]:
>System has non-zero total charge: -0.189598
>Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>for discussion on how close it should be to an integer.
>  WARNING 1 [file topol.top, line 55]:
>You are using Ewald electrostatics in a system with net charge. This can
>lead to severe artifacts, such as ions moving into regions with low
>dielectric, due to the uniform background charge. We suggest to
>neutralize your system with counter ions, possibly in combination with a
>physiological salt concentration.
>
>  It seems that the -0.189598 non-zero charge causes the fatal error. Is it
> possible to correct it? and how? or could I use the -maxwarn option as
> mentioned in the error message?
>
>  Best regards
>  --
>  Gromacs Users mailing list
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Re: [gmx-users] How to deal with "non-zero total charge" problem in gromacs?

[sunyeping]

I don't know where the non-integral charges come from. But When preparing the 
gro file from the initial PDB file (a protein-DNA complex), I got a information 
saying that there are 24 atoms missing in the structure, but I can't tell what 
are these atoms. Could you tell me how to fix the atom missing problem? Thank 
you. 
--
From:孙业平 
Sent At:2019 Aug. 1 (Thu.) 13:18
To:gromacs.org_gmx-users ; Bratin 
Kumar Das <177cy500.bra...@nitk.edu.in>
Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem in 
gromacs?



--
From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
Sent At:2019 Aug. 1 (Thu.) 12:31
To:gromacs ; 孙业平 
Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem in 
gromacs?

Hi,
Yes you can use the (-maxwarn) flag to overcome the error. But better to 
optimize the starting structure to reduce the excess charge of your system.

Thank you for the replay. But I have no idea of how to optimize the starting 
structure to reduce the excess charge. Could you give me some hints or examples 
or something?

Best regards



On Thu, Aug 1, 2019 at 9:35 AM sunyeping  wrote:
Dear all,

 I am trying to do MD simulation with protein-DNA complex with gromacs. When 
using gmx grompp to generate the tpr file for energy minimization, I enconters 
a fatal error:

 Fatal error:
 Too many warnings (1).
 If you are sure all warnings are harmless, use the -maxwarn option.

 There are two notes and one warning arose with grompp, and they are:

 NOTE 1 [file em.mdp]:
   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
   that with the Verlet scheme, nstlist has no effect on the accuracy of
   your simulation.
 NOTE 2 [file topol.top, line 55]:
   System has non-zero total charge: -0.189598
   Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer.
 WARNING 1 [file topol.top, line 55]:
   You are using Ewald electrostatics in a system with net charge. This can
   lead to severe artifacts, such as ions moving into regions with low
   dielectric, due to the uniform background charge. We suggest to
   neutralize your system with counter ions, possibly in combination with a
   physiological salt concentration.

 It seems that the -0.189598 non-zero charge causes the fatal error. Is it 
possible to correct it? and how? or could I use the -maxwarn option as 
mentioned in the error message?

 Best regards
 -- 
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Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Justin Lemkul]

On 8/1/19 7:04 PM, Mohammed I Sorour wrote:

Hi,


that's what the ls -l prints,





ls -l
total 193120
drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff
-rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
-rw-r--r-- 1 tuf73544 chem  191 Aug  1 15:04 equilibration_NVT_script
-rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro
-rw-r--r-- 1 tuf73544 chem 2164 Jul  8  2016 ions.itp
-rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr
-rw-r--r-- 1 tuf73544 chem11962 Aug  1 14:57 mdout.mdp
-rw-r--r-- 1 tuf73544 chem11962 Aug  1 14:56 #mdout.mdp.1#
-rw-r--r-- 1 tuf73544 chem 1875 Jul 27 08:22 nvt.mdp
-rw-r--r-- 1 tuf73544 chem 39455312 Aug  1 14:57 nvt.tpr
-rw--- 1 tuf73544 chem 1032 Aug  1 15:04 out
-rw--- 1 tuf73544 chem 2395 Aug  1 15:04 out.err
-rw-r--r-- 1 tuf73544 chem38899 Jul 31 18:58 posre_DNA_chain_A.itp
-rw-r--r-- 1 tuf73544 chem39953 Jul 31 18:58 posre_DNA_chain_B.itp
-rw-r--r-- 1 tuf73544 chem 3215 Aug  1 14:57 residuetypes.dat
-rw-r--r-- 1 tuf73544 chem 4873 Jul 18 13:03 specbond.dat
-rw-r--r-- 1 tuf73544 chem69176 Jul 16 11:40 tip3p.gro
-rw-r--r-- 1 tuf73544 chem   588482 Jul 31 18:58 topol_DNA_chain_A.itp
-rw-r--r-- 1 tuf73544 chem   589283 Jul 31 18:58 topol_DNA_chain_B.itp
-rw--- 1 tuf73544 chem 1264 Jul 31 19:10 topol.top
drwxr-xr-x 3 tuf73544 chem 4096 Aug  1 14:18 trial


Are you executing mdrun interactively, or via some kind of queuing 
system with a submission script?


Also you should *not* be running dynamics on a system with such a net 
charge. Add salt and neutralize! It's not the source of your problem, 
though.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] OPLS parameterization for a modified aminoacid

[Neena Susan Eappen]

Hello gromacs users,

I want to thoroughly learn how OPLS parameters were found for modified 
aminoacids (for instance aspartic acid versus neutral aspartic acid). I am 
currently having unluck using DFT for parameterization.

Any help appreciated,
Neena

From: Neena Susan Eappen
Sent: Wednesday, July 31, 2019 11:54 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [gmx-users] OPLS parameterization for a modified aminoacid

Hello gromacs users,

Do I use this reference for the procedure to find OPLS parameters for a 
modified aminoacid?

Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jorgensen, W.L.: Evaluation 
and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison 
with Accurate Quantum Chemical Calculations on Peptides †. J. Phys. Chem. B. 
105, 6474–6487 (2001).

Many thanks,
Neena
Graduate Student
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Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Mohammed I Sorour]

>
> Hi,


that's what the ls -l prints,

>




> ls -l
> total 193120
> drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff
> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
> -rw-r--r-- 1 tuf73544 chem  191 Aug  1 15:04 equilibration_NVT_script
> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro
> -rw-r--r-- 1 tuf73544 chem 2164 Jul  8  2016 ions.itp
> -rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr
> -rw-r--r-- 1 tuf73544 chem11962 Aug  1 14:57 mdout.mdp
> -rw-r--r-- 1 tuf73544 chem11962 Aug  1 14:56 #mdout.mdp.1#
> -rw-r--r-- 1 tuf73544 chem 1875 Jul 27 08:22 nvt.mdp
> -rw-r--r-- 1 tuf73544 chem 39455312 Aug  1 14:57 nvt.tpr
> -rw--- 1 tuf73544 chem 1032 Aug  1 15:04 out
> -rw--- 1 tuf73544 chem 2395 Aug  1 15:04 out.err
> -rw-r--r-- 1 tuf73544 chem38899 Jul 31 18:58 posre_DNA_chain_A.itp
> -rw-r--r-- 1 tuf73544 chem39953 Jul 31 18:58 posre_DNA_chain_B.itp
> -rw-r--r-- 1 tuf73544 chem 3215 Aug  1 14:57 residuetypes.dat
> -rw-r--r-- 1 tuf73544 chem 4873 Jul 18 13:03 specbond.dat
> -rw-r--r-- 1 tuf73544 chem69176 Jul 16 11:40 tip3p.gro
> -rw-r--r-- 1 tuf73544 chem   588482 Jul 31 18:58 topol_DNA_chain_A.itp
> -rw-r--r-- 1 tuf73544 chem   589283 Jul 31 18:58 topol_DNA_chain_B.itp
> -rw--- 1 tuf73544 chem 1264 Jul 31 19:10 topol.top
> drwxr-xr-x 3 tuf73544 chem 4096 Aug  1 14:18 trial
>

Thanks,
Mohammed
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Re: [gmx-users] best performance on GPU

[Mark Abraham]

Hi,

We can't tell whether or what the problem is without more information.
Please upload your .log file to a file sharing service and post a link.

Mark

On Fri, 2 Aug 2019 at 01:05, Maryam  wrote:

> Dear all
> I want to run a simulation of approximately 12000 atoms system in gromacs
> 2016.6 on GPU with the following machine structure:
> Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP
> support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD
> instructions: AVX2_256 FFT library:
> fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG
> support: enabled Hwloc support: disabled Tracing support: disabled Built
> on: Fri Jun 21 09:58:11 EDT 2019 Built by: julian@BioServer [CMAKE] Build
> OS/arch: Linux 4.15.0-52-generic x86_64 Build CPU vendor: AMD Build CPU
> brand: AMD Ryzen 7 1800X Eight-Core Processor Build CPU family: 23 Model: 1
> Stepping: 1
> Number of GPUs detected: 1 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.:
> 7.5, ECC: no, stat: compatible
> i used different commands to get the best performance and i dont know which
> point i am missing. the quickest time possible is got by this command:gmx
> mdrun -s md.tpr -nb gpu -deffnm MD -tunepme -v
> which is 10 ns/day! and it takes 2 months to end.
>  though i used several commands to tune it like: gmx mdrun -ntomp 6 -pin on
> -resethway -nstlist 20 -s md.tpr -deffnm md -cpi md.cpt -tunepme -cpt 15
> -append -gpu_id 0 -nb auto.  In the gromacs website it is mentioned that
> with this properties I should be able to run it in  295 ns/day!
> could you help me find out what point i am missing that i can not reach the
> best performance level?
> Thank you
> --
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>
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Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Mark Abraham]

Hi,

What does ls -l return when run from your working directory?

Mark

On Fri, 2 Aug 2019 at 01:49, Mohammed I Sorour 
wrote:

> Hello Dr. Dallas,
>
> Yes, the nvt.tpr was created and I had it in the local directory ready for
> the mdrun.
> Yes, those copy/pastes of the commands I used.
> Since I'm kind of new to the MD simulations, so I'm sticking to that
> tutorial
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
> .
> Also, I tried to use the mdrun command in a different way just to give it a
> try
>
> command: gmx mdrun -s nvt.tpr -deffnm nvt
>
> It gave me the following error.
>
> Error in user input:
> Invalid command-line options
>   In command-line option -s
> File 'nvt.tpr' does not exist or is not accessible.
> The file could not be opened.
>   Reason: No such file or directory
>   (call to fopen() returned error code 2)
>
> I know that it is clearly saying that nvt.tpr is not there. But I'm also
> sure that I have it there.
>
> Thanks,
> Mohammed
>
> On Thu, Aug 1, 2019 at 6:40 PM Dallas Warren 
> wrote:
>
> > From that command, was the nvt.tpr actually created? Can you see it in
> the
> > directory? What happens if you type in the files for each of the command
> > switches instead of using -deffnm to autocomplete them for you?
> >
> > Are those copy/pastes of the commands you used?
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Delivery, Disposition and Dynamics
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.war...@monash.edu
> > -
> > When the only tool you own is a hammer, every problem begins to resemble
> a
> > nail.
> >
> >
> > On Fri, 2 Aug 2019 at 08:30, Mohammed I Sorour <
> mohammed.sor...@temple.edu
> > >
> > wrote:
> >
> > > Hi Justin,
> > >
> > >  Thank you so much for your reply.
> > >
> > > for the NVT run, I used the following commands
> > >
> > > *gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr*
> > >
> > > which generated the nvt.tpr file and printed the following:
> > >
> > > Ignoring obsolete mdp entry 'title'
> > >
> > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> > > Setting the LD random seed to 708625668
> > > Generated 4851 of the 4851 non-bonded parameter combinations
> > > Generating 1-4 interactions: fudge = 0.5
> > > Generated 4851 of the 4851 1-4 parameter combinations
> > > Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
> > > turning all bonds into constraints...
> > > Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
> > > turning all bonds into constraints...
> > > Excluding 2 bonded neighbours molecule type 'SOL'
> > > turning all bonds into constraints...
> > > Excluding 1 bonded neighbours molecule type 'MG'
> > > turning all bonds into constraints...
> > > Excluding 1 bonded neighbours molecule type 'CL'
> > > turning all bonds into constraints...
> > >
> > > NOTE 1 [file topol.top, line 51]:
> > >   System has non-zero total charge: -117.68
> > >   Total charge should normally be an integer. See
> > >   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > >   for discussion on how close it should be to an integer.
> > >
> > >
> > >
> > > Setting gen_seed to -1290262031
> > > Velocities were taken from a Maxwell distribution at 300 K
> > > Removing all charge groups because cutoff-scheme=Verlet
> > > Analysing residue names:
> > > There are:   124DNA residues
> > > There are: 455308  Water residues
> > > Number of degrees of freedom in T-Coupling group DNA is 7631.99
> > > Number of degrees of freedom in T-Coupling group Water is 2724393.00
> > > Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
> > > Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036
> nm
> > > Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000
> nm
> > > Note that mdrun will redetermine rlist based on the actual pair-list
> > setup
> > > Calculating fourier grid dimensions for X Y Z
> > > Using a fourier grid of 160x160x160, spacing 0.150 0.150 0.150
> > > Estimate for the relative computational load of the PME mesh part: 0.16
> > >
> > > NOTE 2 [file nvt.mdp]:
> > >   This run will generate roughly 31380 Mb of data
> > >
> > >
> > > There were 2 notes
> > >
> > > GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa)
> > >
> > > *Then I used the mdrun command *
> > >
> > > *gmx mdrun -deffnm nvt*
> > >
> > >
> > >
> > > Again, I have run a couple of systems before that and I successfully
> ran
> > > the MD_production calculation, following the same procedure. The only
> > > difference I could notice is the charges rounding, because it didn't
> > happen
> > > with those that ran successfully. That is why I suspected that.
> > >
> > > Please, let me know if I need to provide more information.
> > >
> > > Thanks,
> > >
> > > Mohammed
> > >
> > >
> > > On Thu, Aug 1, 2019 at 3:52 PM 

Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Mohammed I Sorour]

Hello Dr. Dallas,

Yes, the nvt.tpr was created and I had it in the local directory ready for
the mdrun.
Yes, those copy/pastes of the commands I used.
Since I'm kind of new to the MD simulations, so I'm sticking to that
tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
.
Also, I tried to use the mdrun command in a different way just to give it a
try

command: gmx mdrun -s nvt.tpr -deffnm nvt

It gave me the following error.

Error in user input:
Invalid command-line options
  In command-line option -s
File 'nvt.tpr' does not exist or is not accessible.
The file could not be opened.
  Reason: No such file or directory
  (call to fopen() returned error code 2)

I know that it is clearly saying that nvt.tpr is not there. But I'm also
sure that I have it there.

Thanks,
Mohammed

On Thu, Aug 1, 2019 at 6:40 PM Dallas Warren 
wrote:

> From that command, was the nvt.tpr actually created? Can you see it in the
> directory? What happens if you type in the files for each of the command
> switches instead of using -deffnm to autocomplete them for you?
>
> Are those copy/pastes of the commands you used?
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
> On Fri, 2 Aug 2019 at 08:30, Mohammed I Sorour  >
> wrote:
>
> > Hi Justin,
> >
> >  Thank you so much for your reply.
> >
> > for the NVT run, I used the following commands
> >
> > *gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr*
> >
> > which generated the nvt.tpr file and printed the following:
> >
> > Ignoring obsolete mdp entry 'title'
> >
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> > Setting the LD random seed to 708625668
> > Generated 4851 of the 4851 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 4851 of the 4851 1-4 parameter combinations
> > Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
> > turning all bonds into constraints...
> > Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
> > turning all bonds into constraints...
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > turning all bonds into constraints...
> > Excluding 1 bonded neighbours molecule type 'MG'
> > turning all bonds into constraints...
> > Excluding 1 bonded neighbours molecule type 'CL'
> > turning all bonds into constraints...
> >
> > NOTE 1 [file topol.top, line 51]:
> >   System has non-zero total charge: -117.68
> >   Total charge should normally be an integer. See
> >   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> >   for discussion on how close it should be to an integer.
> >
> >
> >
> > Setting gen_seed to -1290262031
> > Velocities were taken from a Maxwell distribution at 300 K
> > Removing all charge groups because cutoff-scheme=Verlet
> > Analysing residue names:
> > There are:   124DNA residues
> > There are: 455308  Water residues
> > Number of degrees of freedom in T-Coupling group DNA is 7631.99
> > Number of degrees of freedom in T-Coupling group Water is 2724393.00
> > Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
> > Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036 nm
> > Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
> > Note that mdrun will redetermine rlist based on the actual pair-list
> setup
> > Calculating fourier grid dimensions for X Y Z
> > Using a fourier grid of 160x160x160, spacing 0.150 0.150 0.150
> > Estimate for the relative computational load of the PME mesh part: 0.16
> >
> > NOTE 2 [file nvt.mdp]:
> >   This run will generate roughly 31380 Mb of data
> >
> >
> > There were 2 notes
> >
> > GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa)
> >
> > *Then I used the mdrun command *
> >
> > *gmx mdrun -deffnm nvt*
> >
> >
> >
> > Again, I have run a couple of systems before that and I successfully ran
> > the MD_production calculation, following the same procedure. The only
> > difference I could notice is the charges rounding, because it didn't
> happen
> > with those that ran successfully. That is why I suspected that.
> >
> > Please, let me know if I need to provide more information.
> >
> > Thanks,
> >
> > Mohammed
> >
> >
> > On Thu, Aug 1, 2019 at 3:52 PM Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 8/1/19 3:50 PM, Mohammed I Sorour wrote:
> > > > Dear Gromacs users,
> > > >
> > > > I'm running MD simulation on a couple of DNA systems that only vary
> in
> > > > sequence. Most of the runs worked just fine, but surprisingly I have
> > one
> > > > system that I got an error in the NVT equilibration step.
> > > > I'm following the
> > > > tutorialhttp://
> > >
> >
> 

Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Dallas Warren]

>From that command, was the nvt.tpr actually created? Can you see it in the
directory? What happens if you type in the files for each of the command
switches instead of using -deffnm to autocomplete them for you?

Are those copy/pastes of the commands you used?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 2 Aug 2019 at 08:30, Mohammed I Sorour 
wrote:

> Hi Justin,
>
>  Thank you so much for your reply.
>
> for the NVT run, I used the following commands
>
> *gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr*
>
> which generated the nvt.tpr file and printed the following:
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> Setting the LD random seed to 708625668
> Generated 4851 of the 4851 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 4851 of the 4851 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
> turning all bonds into constraints...
> Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
> turning all bonds into constraints...
> Excluding 2 bonded neighbours molecule type 'SOL'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'MG'
> turning all bonds into constraints...
> Excluding 1 bonded neighbours molecule type 'CL'
> turning all bonds into constraints...
>
> NOTE 1 [file topol.top, line 51]:
>   System has non-zero total charge: -117.68
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
>
>
>
> Setting gen_seed to -1290262031
> Velocities were taken from a Maxwell distribution at 300 K
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are:   124DNA residues
> There are: 455308  Water residues
> Number of degrees of freedom in T-Coupling group DNA is 7631.99
> Number of degrees of freedom in T-Coupling group Water is 2724393.00
> Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
> Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036 nm
> Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
> Note that mdrun will redetermine rlist based on the actual pair-list setup
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 160x160x160, spacing 0.150 0.150 0.150
> Estimate for the relative computational load of the PME mesh part: 0.16
>
> NOTE 2 [file nvt.mdp]:
>   This run will generate roughly 31380 Mb of data
>
>
> There were 2 notes
>
> GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa)
>
> *Then I used the mdrun command *
>
> *gmx mdrun -deffnm nvt*
>
>
>
> Again, I have run a couple of systems before that and I successfully ran
> the MD_production calculation, following the same procedure. The only
> difference I could notice is the charges rounding, because it didn't happen
> with those that ran successfully. That is why I suspected that.
>
> Please, let me know if I need to provide more information.
>
> Thanks,
>
> Mohammed
>
>
> On Thu, Aug 1, 2019 at 3:52 PM Justin Lemkul  wrote:
>
> >
> >
> > On 8/1/19 3:50 PM, Mohammed I Sorour wrote:
> > > Dear Gromacs users,
> > >
> > > I'm running MD simulation on a couple of DNA systems that only vary in
> > > sequence. Most of the runs worked just fine, but surprisingly I have
> one
> > > system that I got an error in the NVT equilibration step.
> > > I'm following the
> > > tutorialhttp://
> >
> www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
> > >
> > > rogram: gmx mdrun, version 2016.3
> > > Source file: src/gromacs/options/options.cpp (line 258)
> > > Function:void gmx::Options::finish()
> > >
> > > Error in user input:
> > > Invalid input values
> > >In option s
> > >  Required option was not provided, and the default file 'topol'
> does
> > not
> > >  exist or is not accessible.
> > >  The following extensions were tried to complete the file name:
> > >.tpr
> > >
> > > I'm pretty sure that I have the .tpr  files in the local directory. I
> > have
> > > read the previous reviews of the Gromacs mailing list, and I know that
> > > it would be a problem with the toplogy file. The toplogy files looks
> > > so far good to me.
> >
> > There's a typo in your command or the input file you think is there is
> > not. You didn't provide your mdrun command (please always do this) but I
> > suspect the former. If mdrun does not find the file you specify, it
> > looks for the default file name, which is topol.tpr. That's also not
> > there, so you get a fatal error.
> >
> > > 

Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Mohammed I Sorour]

Hi Justin,

 Thank you so much for your reply.

for the NVT run, I used the following commands

*gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr*

which generated the nvt.tpr file and printed the following:

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Setting the LD random seed to 708625668
Generated 4851 of the 4851 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 4851 of the 4851 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'DNA_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'DNA_chain_A'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'MG'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'CL'
turning all bonds into constraints...

NOTE 1 [file topol.top, line 51]:
  System has non-zero total charge: -117.68
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Setting gen_seed to -1290262031
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   124DNA residues
There are: 455308  Water residues
Number of degrees of freedom in T-Coupling group DNA is 7631.99
Number of degrees of freedom in T-Coupling group Water is 2724393.00
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 160x160x160, spacing 0.150 0.150 0.150
Estimate for the relative computational load of the PME mesh part: 0.16

NOTE 2 [file nvt.mdp]:
  This run will generate roughly 31380 Mb of data


There were 2 notes

GROMACS reminds you: "Push It Real Good" (Salt 'n' Pepa)

*Then I used the mdrun command *

*gmx mdrun -deffnm nvt*



Again, I have run a couple of systems before that and I successfully ran
the MD_production calculation, following the same procedure. The only
difference I could notice is the charges rounding, because it didn't happen
with those that ran successfully. That is why I suspected that.

Please, let me know if I need to provide more information.

Thanks,

Mohammed


On Thu, Aug 1, 2019 at 3:52 PM Justin Lemkul  wrote:

>
>
> On 8/1/19 3:50 PM, Mohammed I Sorour wrote:
> > Dear Gromacs users,
> >
> > I'm running MD simulation on a couple of DNA systems that only vary in
> > sequence. Most of the runs worked just fine, but surprisingly I have one
> > system that I got an error in the NVT equilibration step.
> > I'm following the
> > tutorialhttp://
> www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html
> >
> > rogram: gmx mdrun, version 2016.3
> > Source file: src/gromacs/options/options.cpp (line 258)
> > Function:void gmx::Options::finish()
> >
> > Error in user input:
> > Invalid input values
> >In option s
> >  Required option was not provided, and the default file 'topol' does
> not
> >  exist or is not accessible.
> >  The following extensions were tried to complete the file name:
> >.tpr
> >
> > I'm pretty sure that I have the .tpr  files in the local directory. I
> have
> > read the previous reviews of the Gromacs mailing list, and I know that
> > it would be a problem with the toplogy file. The toplogy files looks
> > so far good to me.
>
> There's a typo in your command or the input file you think is there is
> not. You didn't provide your mdrun command (please always do this) but I
> suspect the former. If mdrun does not find the file you specify, it
> looks for the default file name, which is topol.tpr. That's also not
> there, so you get a fatal error.
>
> > Here is the only thing I can susbect, but I don't know if this is the
> > cause, but also I'm still wondering why: So When I generated my ssytem
> > topology using pdb2gmx
> >
> >
> > "Now there are 3969 atoms and 124 residues
> > Total mass in system 37825.764 a.m.u.
> > Total charge in system -118.000 e"
> >
> > But when I start the solvation, the total charge of the system changes
> > and is no more an intger:
> >
> > "NOTE 2 [file topol.top, line 51]:
> >System has non-zero total charge: -117.68
> >Total charge should normally be an integer. See
> >http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> >for discussion on how close it should be to an integer."
> >  From the gromacs documentations, it's fine to have that slight
> > non-integer charge, but I'm wondering why is that happening?!
>
> You have a 

[gmx-users] best performance on GPU

[Maryam]

Dear all
I want to run a simulation of approximately 12000 atoms system in gromacs
2016.6 on GPU with the following machine structure:
Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP
support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD
instructions: AVX2_256 FFT library:
fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG
support: enabled Hwloc support: disabled Tracing support: disabled Built
on: Fri Jun 21 09:58:11 EDT 2019 Built by: julian@BioServer [CMAKE] Build
OS/arch: Linux 4.15.0-52-generic x86_64 Build CPU vendor: AMD Build CPU
brand: AMD Ryzen 7 1800X Eight-Core Processor Build CPU family: 23 Model: 1
Stepping: 1
Number of GPUs detected: 1 #0: NVIDIA GeForce RTX 2080 Ti, compute cap.:
7.5, ECC: no, stat: compatible
i used different commands to get the best performance and i dont know which
point i am missing. the quickest time possible is got by this command:gmx
mdrun -s md.tpr -nb gpu -deffnm MD -tunepme -v
which is 10 ns/day! and it takes 2 months to end.
 though i used several commands to tune it like: gmx mdrun -ntomp 6 -pin on
-resethway -nstlist 20 -s md.tpr -deffnm md -cpi md.cpt -tunepme -cpt 15
-append -gpu_id 0 -nb auto.  In the gromacs website it is mentioned that
with this properties I should be able to run it in  295 ns/day!
could you help me find out what point i am missing that i can not reach the
best performance level?
Thank you
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Re: [gmx-users] How to deal with "non-zero total charge" problem in gromacs?

[Dallas Warren]

Go through the topologies, residue by residue, find where it deviates. Each
residue should sum to an integer charge.

Also look at how you generated the topology, actually steps involved, where
the coordinate files came from etc. Somewhere a choice has been made,
process performed that introduced this problem.

On Thu, 1 Aug. 2019, 3:18 pm sunyeping,  wrote:

>
>
> --
> From:Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> Sent At:2019 Aug. 1 (Thu.) 12:31
> To:gromacs ; 孙业平 
> Subject:Re: [gmx-users] How to deal with "non-zero total charge" problem
> in gromacs?
>
> Hi,
> Yes you can use the (-maxwarn) flag to overcome the error. But better
> to optimize the starting structure to reduce the excess charge of your
> system.
>
> Thank you for the replay. But I have no idea of how to optimize the
> starting structure to reduce the excess charge. Could you give me some
> hints or examples or something?
>
> Best regards
>
>
>
> On Thu, Aug 1, 2019 at 9:35 AM sunyeping  wrote:
> Dear all,
>
>  I am trying to do MD simulation with protein-DNA complex with gromacs.
> When using gmx grompp to generate the tpr file for energy minimization, I
> enconters a fatal error:
>
>  Fatal error:
>  Too many warnings (1).
>  If you are sure all warnings are harmless, use the -maxwarn option.
>
>  There are two notes and one warning arose with grompp, and they are:
>
>  NOTE 1 [file em.mdp]:
>With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>that with the Verlet scheme, nstlist has no effect on the accuracy of
>your simulation.
>  NOTE 2 [file topol.top, line 55]:
>System has non-zero total charge: -0.189598
>Total charge should normally be an integer. See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>for discussion on how close it should be to an integer.
>  WARNING 1 [file topol.top, line 55]:
>You are using Ewald electrostatics in a system with net charge. This can
>lead to severe artifacts, such as ions moving into regions with low
>dielectric, due to the uniform background charge. We suggest to
>neutralize your system with counter ions, possibly in combination with a
>physiological salt concentration.
>
>  It seems that the -0.189598 non-zero charge causes the fatal error. Is it
> possible to correct it? and how? or could I use the -maxwarn option as
> mentioned in the error message?
>
>  Best regards
>  --
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Re: [gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Justin Lemkul]

On 8/1/19 3:50 PM, Mohammed I Sorour wrote:

Dear Gromacs users,

I'm running MD simulation on a couple of DNA systems that only vary in
sequence. Most of the runs worked just fine, but surprisingly I have one
system that I got an error in the NVT equilibration step.
I'm following the
tutorialhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html

rogram: gmx mdrun, version 2016.3
Source file: src/gromacs/options/options.cpp (line 258)
Function:void gmx::Options::finish()

Error in user input:
Invalid input values
   In option s
 Required option was not provided, and the default file 'topol' does not
 exist or is not accessible.
 The following extensions were tried to complete the file name:
   .tpr

I'm pretty sure that I have the .tpr  files in the local directory. I have
read the previous reviews of the Gromacs mailing list, and I know that
it would be a problem with the toplogy file. The toplogy files looks
so far good to me.


There's a typo in your command or the input file you think is there is 
not. You didn't provide your mdrun command (please always do this) but I 
suspect the former. If mdrun does not find the file you specify, it 
looks for the default file name, which is topol.tpr. That's also not 
there, so you get a fatal error.



Here is the only thing I can susbect, but I don't know if this is the
cause, but also I'm still wondering why: So When I generated my ssytem
topology using pdb2gmx


"Now there are 3969 atoms and 124 residues
Total mass in system 37825.764 a.m.u.
Total charge in system -118.000 e"

But when I start the solvation, the total charge of the system changes
and is no more an intger:

"NOTE 2 [file topol.top, line 51]:
   System has non-zero total charge: -117.68
   Total charge should normally be an integer. See
   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
   for discussion on how close it should be to an integer."
 From the gromacs documentations, it's fine to have that slight
non-integer charge, but I'm wondering why is that happening?!


You have a large system with a lot of charges. You're going to 
accumulate rounding error. This is not a problem.


-Justin


I ran the energy minimization using these files, and it worked well,
it only failing with the NVT step.

I deeply aplogize for the lenghty email and for submitting the same
email previously. The first one was not complete and was sent by
mistake.

Sincerely,

Mohammed Sorour


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

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[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Mohammed I Sorour]

Dear Gromacs users,

I'm running MD simulation on a couple of DNA systems that only vary in
sequence. Most of the runs worked just fine, but surprisingly I have one
system that I got an error in the NVT equilibration step.
I'm following the
tutorialhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html

rogram: gmx mdrun, version 2016.3
Source file: src/gromacs/options/options.cpp (line 258)
Function:void gmx::Options::finish()

Error in user input:
Invalid input values
  In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
  .tpr

I'm pretty sure that I have the .tpr  files in the local directory. I have
read the previous reviews of the Gromacs mailing list, and I know that
it would be a problem with the toplogy file. The toplogy files looks
so far good to me.

Here is the only thing I can susbect, but I don't know if this is the
cause, but also I'm still wondering why: So When I generated my ssytem
topology using pdb2gmx


"Now there are 3969 atoms and 124 residues
Total mass in system 37825.764 a.m.u.
Total charge in system -118.000 e"

But when I start the solvation, the total charge of the system changes
and is no more an intger:

"NOTE 2 [file topol.top, line 51]:
  System has non-zero total charge: -117.68
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer."
>From the gromacs documentations, it's fine to have that slight
non-integer charge, but I'm wondering why is that happening?!

I ran the energy minimization using these files, and it worked well,
it only failing with the NVT step.

I deeply aplogize for the lenghty email and for submitting the same
email previously. The first one was not complete and was sent by
mistake.

Sincerely,

Mohammed Sorour
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[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible

[Mohammed I Sorour]

Dear Gromacs users,

I'm running MD simulation on a couple of DNA systems that only vary in
sequence. Most of the runs worked just fine, but surprisingly I have one
system that I got an error in the NVT equilibration step.
I'm following the tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html

rogram: gmx mdrun, version 2016.3
Source file: src/gromacs/options/options.cpp (line 258)
Function:void gmx::Options::finish()

Error in user input:
Invalid input values
  In option s
Required option was not provided, and the default file 'topol' does not
exist or is not accessible.
The following extensions were tried to complete the file name:
  .tpr

I'm pretty sure that I have the .tpr  files in the local directory. I have
read the previous reviews of the Gromacs mailing list, but I
-- 
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[gmx-users] Equilibration Error, Skew Factor

[Hemant Khoba]

Hello,

I am working on a coarse-grained polymer system having various chain length
(20 & 62), dissolved in water with different counter-ion concentrations.
While equilibrating the systems I am consistently facing an error.

For chain Length 20;
Fatal error:
The X-size of the box (6.716921) times the triclinic skew factor (1.00)
is
smaller than the number of DD cells (4) times the smallest allowed cell size
(1.68)

For chain length 62;
Fatal error:
The X-size of the box (11.840870) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (8) times the smallest allowed cell
size (1.48)

I have accurately calculated the box size to maintain a particular ion
concentration. 9.8 cubic box for chain length 20 and 18 nm cubic box for
chain length 62.

attached are the .mdp's for temperature and pressure equilibration. Any
suggestions would be highly appreciated.

Thanking you in advance.


Regards,
Hemant Khoba


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08/01/19,
05:42:21 PM
; minim.mdp - used as input into grompp to generate em.tpr
;
; Run parameters
integrator   = steep; Algorithm (steep = steepest 
descent minimization)
tinit= 0
dt   = 0.002
init-step= 0
comm-mode= Linear
nstcomm  = 100
comm-grps= system
emtol= 1000.0   ; Stop 
minimization when the maximum force < 1000.0 kJ/mol/nm
emstep   = 0.002; Energy step size
nsteps   = 5; Maximum number of 
(minimization) steps to perform
;
; Output control
nstxout   = 500 ; save coordinates every 1 ps
nstvout   = 500 ; save velocities every 1 ps
nstenergy = 500 ; save energies every 1 ps
nstxtcout = 500 ; co-ordinates to xtc
nstlog= 500 ; update log file every 1.0 ps
nstfout   = 500
nstcalcenergy = 100 ; calculate energies
nstcheckpoint = 1000
xtc-precision = 1000
xtc_grps  = system
;
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = -1
;
; Max number of iterations in relax_shells
niter= 20
;
; NEIGHBOR SEARCHING
cutoff-scheme= Verlet
ns-type  = grid ; Method to determine 
neighbor list (simple, grid)
nstlist  = 10   ; Frequency to update the 
neighbor list and long range forces
rlist= 1.0
rvdw = 1.0  ; Short-range 
Van der Waals cut-off
verlet-buffer-tolerance  = 0.005
pbc  = xyz  ; Periodic 
Boundary Conditions (yes/no)
periodic_molecules   = no
;
; ELECTROSTATICS
coulombtype  = PME  ; Treatment of 
long range electrostatic interactions
pme-order= 8
rcoulomb = 1.2  ; Short-range 
electrostatic cut-off
rcoulomb-switch  = 0
epsilon-r= 1; 2.5 (with polarizable water)
epsilon-rf   = 1
;
; VAN DER WAALS
vdwtype  = Cut-off
vdw-modifier = Potential-shift-verlet
;
; CUT-OFF LENGHTS   
rvdw-switch  = 0
;
; Ewald
DispCorr = EnerPres ;Apply long range dispersion 
corrections for Energy and Pressure
table-extension  = 1
energygrp-table  = 
fourierspacing   = 0.15
fourier-nx   = 0
fourier-ny   = 0
fourier-nz   = 0
ewald-rtol   = 1e-05
ewald-rtol-lj= 1e-3
ewald-geometry   = 3d
lj-pme-comb-rule = Geometric
epsilon-surface  = 0
optimize_fft = yes
;
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl   = No
tc-grps  = 
tau-t= 
ref-t= 
pcoupl   = No
pcoupltype   = Isotropic
tau-p= 1
ref-p= 
refcoord_scaling = No
andersen_seed= 815131
;
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = no
gen-temp = 300
gen_seed = -1   ;173529
;
; OPTIONS FOR BONDS
constraints  = none
constraint-algorithm = LINCS
continuation = no
Shake-SOR= no
shake-tol= 0.0001
lincs-order  = 8
lincs-iter   = 1
lincs-warnangle  = 30
morse= notitle   = 

Re: [gmx-users] REMD

[Justin Lemkul]

On 7/31/19 1:44 AM, Bratin Kumar Das wrote:

Hi,
 I have some doubt regarding REMD simulation.
 1. In the .mdp file of each replica is it necessary to keep the
gen-temp constant?
as example: 300 k is the lowest temp of REMD simulation. Is it necessary to
keep the gen-temp=300 in each replica.


No, because each subsystem needs to be equilibrated independently at the 
desired temperature.



 2. Is it necessary to provide -replex flag during the equilbration
phase of REMD simulation


No, because these simulations are independent of one another. Only 
during the actual REMD do you need -replex.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] gromacs pullcode

[Justin Lemkul]

On 7/31/19 4:20 AM, zhaox wrote:

Hi,
There are two  groups in my system.When I use the pull code to pull 
one group along the axis X, setting pull_coord1_geometry 
=direction-periodic,I am confused with the "distance at start" and the 
"reference at t=0".Could anyone can tell me how to understand 
these?And if I use the absolute reference,how to understand these? For 
example,when I set the pull_coord1_origin=0 0 0，how to calculate 
“distance at start”？

Thank you in advance.


I answered this exact question some time ago:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-July/125833.html

-Justin


My pull code is followed:
; Pull code
freezegrps          = bot    top
freezedim           = Y Y Y  n y n
pull                = yes
pull_ncoords        = 2         ; two reaction coordinates x and z
pull_ngroups        = 2         ; one group defining one reaction 
coordinate

pull_group1_name    = top
pull_group2_name    = bot
pull_coord1_type    = umbrella    ;harmonic potential
pull_coord1_geometry= direction-periodic
pull_coord1_vec     = 1 0 0
pull_coord1_origin  = 0 0 0
pull_coord1_groups  = 0 1
pull_coord1_start   = yes
pull_coord1_k       = 4000
pull_coord1_rate    = 0.005

pull_coord2_type    = constant-force
pull_coord2_geometry= distance
pull_coord2_dim     = n n y
pull_coord2_groups  = 1 2
pull_coord2_start   = yes
pull_coord2_k       = 3838550        ;KJ mol^-1 nm^-1

pull_group1_pbcatom  = 5806
;pull_group2_pbcatom  = 1887
pull-pbc-ref-prev-step-com = yes



cos-acceleration    = 0.05
comm-mode            = linear
nstcomm              = 10
comm-grps            =


zhaox
zh...@nuaa.edu.cn

 

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定制




--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] GROMOS 54a7 mapping warning

[Justin Lemkul]

On 8/1/19 6:25 AM, Gselman, Larissa wrote:

Thank you for your answer! I used the Yasara -> Edit -> Clean Option and it 
added atoms (1H, 2H and 3H for ASP and OXT for ASN) to my pdb file.


Nevertheless, I still get the same warnings when I try with -ignh. I cannot see 
that there are other atoms missing?


Using -ignh should be fine. The warnings are just pdb2gmx being (in my 
opinion) too noisy. It is telling you that it is applying patches to 
remove those atoms, which is actually what you want. A warning should 
not prevent the topology from being written. If it is, you can move on.


-Justin



When I try without -ignh, I even get a fatal error which says: Atom HA in 
residue ASP 1 was not found in rtp entry ASP with 11 atoms while sorting atoms.


When I look into the aminoacids.rtp file from the GROMOS 54a7 force field it 
looks like this:

[ ASP ]
  [ atoms ]
 N N-0.31000 0
 H H  0.31000 0
 CA   CH1 0.0 1
 CB   CH2 0.0 1
 CG C0.27000 2
 OD1OM-0.63500 2
  OD2OM-0.63500 2
 C C   0.450 3
 O O  -0.450 3



Here are my first and last amino acids from the new pdb file with the added 
atoms:


ATOM  1  N   ASP A   1  59.994  60.432  82.286  1.00  7.49   N
ATOM  2 1H   ASP A   1  60.547  59.791  81.754  1.00  7.49   H
ATOM  3 2H   ASP A   1  59.319  59.903  82.801  1.00  7.49   H
ATOM  4 3H   ASP A   1  60.596  60.885  82.944  1.00  7.49   H
ATOM  5  CA  ASP A   1  59.341  61.407  81.415  1.00  7.49   C
ATOM  6  HA  ASP A   1  58.651  60.833  80.799  1.00  7.49   H
ATOM  7  C   ASP A   1  60.313  62.117  80.435  1.00  7.49   C
ATOM  8  O   ASP A   1  61.524  61.881  80.391  1.00  7.49   O
ATOM  9  CB  ASP A   1  58.494  62.384  82.263  1.00  7.49   C
ATOM 10 1HB  ASP A   1  58.142  61.868  83.157  1.00  7.49   H
ATOM 11 2HB  ASP A   1  59.114  63.222  82.584  1.00  7.49   H
ATOM 12  CG  ASP A   1  57.247  62.920  81.535  1.00  7.49   C
ATOM 13  OD1 ASP A   1  57.107  62.729  80.305  1.00  7.49   O
ATOM 14  OD2 ASP A   1  56.369  63.525  82.180  1.00  7.49   O
.

.

.

ATOM626  N   ASN A  38  49.792  47.722  37.078  1.00 13.81   N
ATOM627  H   ASN A  38  50.649  48.244  36.922  1.00 13.81   H
ATOM628  CA  ASN A  38  48.636  48.172  36.306  1.00 13.81   C
ATOM629  HA  ASN A  38  48.705  49.256  36.233  1.00 13.81   H
ATOM630  C   ASN A  38  47.283  47.875  36.982  1.00 13.81   C
ATOM631  O   ASN A  38  47.185  47.311  38.072  1.00 13.81   O
ATOM632  OXT ASN A  38  46.199  48.179  36.482  1.00 13.81   O
ATOM633  CB  ASN A  38  48.757  47.594  34.881  1.00 13.81   C
ATOM634 1HB  ASN A  38  47.934  47.954  34.264  1.00 13.81   H
ATOM635 2HB  ASN A  38  49.688  47.938  34.433  1.00 13.81   H
ATOM636  CG  ASN A  38  48.756  46.074  34.842  1.00 13.81   C
ATOM637  OD1 ASN A  38  49.775  45.434  34.642  1.00 13.81   O
ATOM638  ND2 ASN A  38  47.621  45.445  35.027  1.00 13.81   N
ATOM639 1HD2 ASN A  38  47.668  44.445  35.083  1.00 13.81   H
ATOM640 2HD2 ASN A  38  46.815  45.983  35.313  1.00 13.81   H
TER 641  ASN A  38
END


Thank you so much for your help.


Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 im Auftrag von David van der 
Spoel 
Gesendet: Mittwoch, 31. Juli 2019 21:21:39
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] GROMOS 54a7 mapping warning

Den 2019-07-31 kl. 15:21, skrev Gselman, Larissa:

Hallo everyone,


I want to simulate a peptide with the Gromos 54a7 force field.

Your structure is missing atoms, please fix and rerun without -ignh.


So, my first command is:

gmx_mpi pdb2gmx -f Mh.pdb -o Mh_processed.gro -water spce -ignh -inter

I choose 14 for the Gromos 54a7 ff, then I choose the protonation state the 
titratable amino acids and for the termini I choose the zwitterionic state (so 
I choose 0 and 0).

But this results in the following warnings:

WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
mapped to an entry in the topology database, but the atom H used in an 
interaction of type angle in that entry is not found in the input file. Perhaps 
your atom and/or residue naming needs to be fixed.

WARNING: WARNING: Residue 38 named ASN of a molecule in the input file was 
mapped to an entry in the topology database, but the atom O used in an 
interaction of type angle in that entry is not found in the input file. Perhaps 
your atom and/or residue naming needs to be fixed.


This is the beginning 

Re: [gmx-users] GROMOS 54a7 mapping warning

[Gselman, Larissa]

Thank you for your answer! I used the Yasara -> Edit -> Clean Option and it 
added atoms (1H, 2H and 3H for ASP and OXT for ASN) to my pdb file.


Nevertheless, I still get the same warnings when I try with -ignh. I cannot see 
that there are other atoms missing?


When I try without -ignh, I even get a fatal error which says: Atom HA in 
residue ASP 1 was not found in rtp entry ASP with 11 atoms while sorting atoms.


When I look into the aminoacids.rtp file from the GROMOS 54a7 force field it 
looks like this:

[ ASP ]
 [ atoms ]
N N-0.31000 0
H H  0.31000 0
CA   CH1 0.0 1
CB   CH2 0.0 1
CG C0.27000 2
OD1OM-0.63500 2
 OD2OM-0.63500 2
C C   0.450 3
O O  -0.450 3



Here are my first and last amino acids from the new pdb file with the added 
atoms:


ATOM  1  N   ASP A   1  59.994  60.432  82.286  1.00  7.49   N
ATOM  2 1H   ASP A   1  60.547  59.791  81.754  1.00  7.49   H
ATOM  3 2H   ASP A   1  59.319  59.903  82.801  1.00  7.49   H
ATOM  4 3H   ASP A   1  60.596  60.885  82.944  1.00  7.49   H
ATOM  5  CA  ASP A   1  59.341  61.407  81.415  1.00  7.49   C
ATOM  6  HA  ASP A   1  58.651  60.833  80.799  1.00  7.49   H
ATOM  7  C   ASP A   1  60.313  62.117  80.435  1.00  7.49   C
ATOM  8  O   ASP A   1  61.524  61.881  80.391  1.00  7.49   O
ATOM  9  CB  ASP A   1  58.494  62.384  82.263  1.00  7.49   C
ATOM 10 1HB  ASP A   1  58.142  61.868  83.157  1.00  7.49   H
ATOM 11 2HB  ASP A   1  59.114  63.222  82.584  1.00  7.49   H
ATOM 12  CG  ASP A   1  57.247  62.920  81.535  1.00  7.49   C
ATOM 13  OD1 ASP A   1  57.107  62.729  80.305  1.00  7.49   O
ATOM 14  OD2 ASP A   1  56.369  63.525  82.180  1.00  7.49   O
.

.

.

ATOM626  N   ASN A  38  49.792  47.722  37.078  1.00 13.81   N
ATOM627  H   ASN A  38  50.649  48.244  36.922  1.00 13.81   H
ATOM628  CA  ASN A  38  48.636  48.172  36.306  1.00 13.81   C
ATOM629  HA  ASN A  38  48.705  49.256  36.233  1.00 13.81   H
ATOM630  C   ASN A  38  47.283  47.875  36.982  1.00 13.81   C
ATOM631  O   ASN A  38  47.185  47.311  38.072  1.00 13.81   O
ATOM632  OXT ASN A  38  46.199  48.179  36.482  1.00 13.81   O
ATOM633  CB  ASN A  38  48.757  47.594  34.881  1.00 13.81   C
ATOM634 1HB  ASN A  38  47.934  47.954  34.264  1.00 13.81   H
ATOM635 2HB  ASN A  38  49.688  47.938  34.433  1.00 13.81   H
ATOM636  CG  ASN A  38  48.756  46.074  34.842  1.00 13.81   C
ATOM637  OD1 ASN A  38  49.775  45.434  34.642  1.00 13.81   O
ATOM638  ND2 ASN A  38  47.621  45.445  35.027  1.00 13.81   N
ATOM639 1HD2 ASN A  38  47.668  44.445  35.083  1.00 13.81   H
ATOM640 2HD2 ASN A  38  46.815  45.983  35.313  1.00 13.81   H
TER 641  ASN A  38
END


Thank you so much for your help.


Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 im Auftrag von David van 
der Spoel 
Gesendet: Mittwoch, 31. Juli 2019 21:21:39
An: gmx-us...@gromacs.org
Betreff: Re: [gmx-users] GROMOS 54a7 mapping warning

Den 2019-07-31 kl. 15:21, skrev Gselman, Larissa:
> Hallo everyone,
>
>
> I want to simulate a peptide with the Gromos 54a7 force field.
Your structure is missing atoms, please fix and rerun without -ignh.
>
>
> So, my first command is:
>
> gmx_mpi pdb2gmx -f Mh.pdb -o Mh_processed.gro -water spce -ignh -inter
>
> I choose 14 for the Gromos 54a7 ff, then I choose the protonation state the 
> titratable amino acids and for the termini I choose the zwitterionic state 
> (so I choose 0 and 0).
>
> But this results in the following warnings:
>
> WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
> mapped to an entry in the topology database, but the atom H used in an 
> interaction of type angle in that entry is not found in the input file. 
> Perhaps your atom and/or residue naming needs to be fixed.
>
> WARNING: WARNING: Residue 38 named ASN of a molecule in the input file was 
> mapped to an entry in the topology database, but the atom O used in an 
> interaction of type angle in that entry is not found in the input file. 
> Perhaps your atom and/or residue naming needs to be fixed.
>
>
> This is the beginning and end of my pdb file with ASP as first and ASN as 
> last amino acid:
>
> ATOM  1  N   ASP A   1  59.994  60.432  82.286  1.00  7.49
> ATOM  2  CA  ASP A   1  59.341  61.407  81.415  1.00  7.49
> ATOM  3  HA  ASP A   1  58.651  60.833  80.799  1.00  7.49
> ATOM  4  CB  ASP A   1