[gmx-users] Gromacs 2018.8 checksum

[András Ferenc WACHA]

Dear Gromacs Developers,

I'm trying to install the 2018.8 version of GROMACS through the Spack
package manager (https://spack.io). They have packaged GROMACS, but I
have noticed a SHA256 checksum mismatch. They have
'3776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebec' on
file, while the file I have downloaded from your site directly (and
verified by the md5sum available there) has
'776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebecf'.
Although I strongly doubt that any attacker could come up with a
counterfeit package having a checksum so very close to the original one,
and suspect that this is simply a typo from the Spack package
maintainers, I would like to ask your opinion about this, just to be on
the safe side (avoiding accidental malware infections like what happened
previously https://github.com/Homebrew/homebrew-cask/issues/33536).

Thank you and kind regards,

Andras

-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group (310)

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences (RCNS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.hu
CREDO SAXS instrument: http://credo.ttk.hu




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Re: [gmx-users] Error: Atoms in the .top are not numbered consecutively

[변진영]

Thank you Sir,. I found the typo in my topol.top file.
So I changed the 'InflatGRO' to 'InflateGRO' and prompted the grompp module.
However I have got the new error:

Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 6538)
 does not match topology (topol.top, 138)

I might know why both the coordinate file (system_inflated.gro) and
topology file(topol.top) have the same number of coordinates.
But in tutorial the system_inflated.gro file is produced by concatenating
the KALP_newbox.gro file and dppc128_whole.gro file, so it's no wonder that
the number of coordinates in system_inflated.gro file is different with the
number of coordinates in topol.top file which is produced by prompting the
gmx pdb2gmx module.

I don' t know what I missed.. Any idea as to what cause this problem?

-jinyoung
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[gmx-users] Intermolecular interactions in RDF

[Apramita Chand]

Dear All,
I have 10 peptides in my system and I want to calculate the peptide-peptide
radial distribution function.
How can I calculate only the intermolecular interactions amongst the
peptides (excluding the intramolecular peaks) without repeating the entire
simulation?
The manual has two options for this: setting -nrexcl or giving -cut option
But I am confused as to what values could be specified for such systems?


Thanks,
Apramita
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[gmx-users] topology can't be generated by pdb2gmx with drude force field embedded

[????]

Hello everyone   There's a problem that's been bothering me for a long time?? 
I've embedded the drude polarizable force field in gromacs via cloning the 
soure code from github. when I tried to generate topology via pdb2gmx, the 
terminal always prompts me for such an error: "Fatal error: Residue 'HOH' not 
found in residue topology database". Actually, I used the swm1024.gro file from 
the charmm's websitehttp://mackerell.umaryland.edu/charmm_drude_ff.shtml, so I 
think there's little possibility of error in the gro file. I chose the SWM4_NDP 
water when prompted a choice.  So how can I fix this problem?  Or where is this 
supported to go wrong? I'm not sure whether the problem is with the drude force 
filed files or my operations? Have anyone else ever met this probelm?  Beat 
RegardsTina
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[gmx-users] topology can't be generated by pdb2gmx with drude force field embedded

[????]

Hello everyone   There's a problem that's been bothering me for a long time?? 
I've embedded the drude polarizable in gromacs via cloning the soure code from 
github. when I tried to generate topology via pdb2gmx, the terminal always 
prompts me for such an error: "Fatal error: Residue 'HOH' not found in residue 
topology database". Actually, I used the swm1024.gro file from the charmm's 
websitehttp://mackerell.umaryland.edu/charmm_drude_ff.shtml, so I think there's 
little possibility of error in the gro file. I chose the SWM4_NDP water when 
prompted a choice. So how can I fix this problem? Beat RegardsTina
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Re: [gmx-users] Regarding system shrunk

[Paul Buscemi]

You did not mention the type of surface, but in real life an extruded polymer 
is under stress and you must restrain the ends. As in real life a heated 
uncrosslinked polymer will shrink. The system probably behaved appropriately

PB

> On Dec 9, 2019, at 11:31 AM, Mijiddorj B  wrote:
> 
> Dear GMX users,
> 
> I study the interaction between polymer and surface interactions. Polymer
> parameters were prepared by cgenff, and the parameters of the surface were
> solved by INTERFACEFF. I performed short simulations, however, the system
> was shrunk. I used the standard mdp file of charmm-gui membrane builder
> excluding the smaller time steps and no-constraints.
> 
> If you have any experience, please advise me on how to solve this problem.
> 
> Best regards,
> 
> Mijiddorj
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[gmx-users] A Gromacs Port of the amber LIPID17 force field

[Zhiyi Wu]

Hi Gmx user,
I have made a gromacs port of the amber LIPID17 force field and the files are 
available at https://zenodo.org/record/3561004.
The user can generate the lipids in amber and use it with the force field 
directly. Or the lipid bilayer can be generated using charms-GUI and a script 
charmmlipid2amber.py is provided to convert the charmm lipid to amber lipid.
This port has also retained the modular feature of the original amber LIPID17 
force field, where the user can custom head group or acryl chain and generate 
topology with the existing head group or acryl chain via pdb2gmx. I have 
parametrised the phosphoinositol head group as an example.
For the details of the force field generation and validation, please refer to 
the GitHub page https://github.com/xiki-tempula/gmx_lipid17.ff.
Kind regards,
Zhiyi Wu
DPhil Candidate
Structural Bioinformatics and Computational Biochemistry Unit
University of Oxford
Email: zhiyi...@msdtc.ox.ac.uk
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Re: [gmx-users] solvent evaporation modeling

[SAKO MIRZAIE]

Dear Anders and Kalil,

Thank you for your answers and for sharing the scripts. I will help a lot.

Best,


On Tue, Dec 3, 2019 at 5:12 PM Anders Støttrup Larsen 
wrote:

> Hi Sako
>
> I did something similar where I dehydrated a system of water molecules, in
> my case a crystal but the principles are the same.
>
> I have uploaded the script at
>
> https://github.com/aslarsen/gromacs_dehydration/blob/master/gromacs_dehydration_MPI_V2.py
>
> It was used in this paper
> https://pubs.acs.org/doi/abs/10.1021/acs.cgd.7b00889
>
> I used gromacs 5.1.4 so you might have to update it to your version and
> set whatever parameters you want.
>
> Best Wishes
> Anders
>
> On Tue, Dec 3, 2019 at 10:36 PM Kalil Bernardino <
> kalil.bernard...@gmail.com> wrote:
>
>>  Dear Sako,
>>
>>
>> Unfortunately I don't have access to the script in the present since I'm
>> in
>> the middle of a travel. But anyway it was done in a specific way for the
>> system that we were working on that time and would need some changes to
>> work with different systems.
>>
>> I can describe to you the general idea here.
>>
>>
>> First, there is two ways to simulate the solvent evaporation and we
>> performed both in the paper André cited. The more physical way, since we
>> were working with a liquid vacuum interface, suppose perpendicular to z
>> direction, was to run a short simulation, save the final structure, check
>> which molecules are above some zcut value, exclude they from your
>> structure, rewrite the topology file to update the number of molecules,
>> run
>> the grompp to produce the new tpr and run a new short simulation. This
>> would be something similar to have a liquid with a vacuum pump at z =
>> zcut,
>> and any molecule that enters the vacuum pump will be removed from the
>> system. For this protocol, you should work with constant volume
>> simulations.
>>
>>
>> The problem with this procedure is that it can be very slow, specially
>> when
>> you have too few solvent remaining or if your system have a small vapor
>> pressure, as is your case since you are working with water. So, if you
>> want
>> to complete dry your system, you can remove molecules randomly in the
>> following way. You may or may not want to create a liquid/vacuum
>> interface,
>> depending if you want to simulate the molecule in some interface or if you
>> want to simulate the bulk of something that in being dried. If you have a
>> vacuum interface, you need to work with NVT simulations, but in order to
>> make a bulk simulation you should do in a NPT ensemble.
>>
>>
>> 1- Equilibrate your system with the solvent
>>
>> 2- Save the final structure
>>
>> 3- Delete some fraction of randomly selected solvent molecules. You can do
>> this directly with some script or can use the gromacs command genion to
>> randomly convert some molecules in some monoatomic specie (for instance,
>> "genion -np 60 -pname DEL" and select the water for replace 60 water
>> molecules with 60 particles with name DEL), make_ndx to generate a index
>> file with a group including every molecules except the specie produced by
>> genion (DEL in the example) and then the editconf reading the index.ndx in
>> order to produce a new .gro file with every molecule except the deleted
>> ones. This .gro will be your initial structure for next step. If you want
>> to use the gromacs commands for this remotion, remember to run the grompp
>> again from your final structure to produce a new tpr file before using
>> genion.
>>
>> 4- Rewrite your topology file in order to update the number of solvent
>> molecules
>>
>> 5- Run grompp and mdrun to do a short simulation with this small numer of
>> water molecules and save the final structure
>>
>> 6- If still have water in your system (or if have more water than you want
>> in your final structure), go back to step 3 and continue removing.
>>
>>
>> You should not remove a large amount of molecules in a single step or this
>> can lead to some artificial structures. And by the end of your process,
>> when you have only a small amount of solvent, I think it is better to
>> reduce even more the amount removed at each step (which is not so bad
>> because your simulation will run faster at this point).
>>
>>
>> Hope this protocol helps you.
>>
>>
>> Best,
>>
>> Kalil
>>
>>
>>
>> Em seg., 2 de dez. de 2019 às 14:14, SAKO MIRZAIE > >
>> escreveu:
>>
>> > Dear André,
>> >
>> > Thank you very much for your email and hope Kalil has the script.
>> >
>> > Best regards
>> >
>> > On Mon, Dec 2, 2019 at 7:15 AM André Farias de Moura 
>> > wrote:
>> >
>> >> Dear Sako,
>> >>
>> >> I'm ccing Kalil, who actually wrote and run the script to remove
>> solvent
>> >> molecules, he might still have it.
>> >>
>> >> regards
>> >>
>> >> Andre
>> >>
>> >> On Mon, Dec 2, 2019 at 2:54 AM SAKO MIRZAIE 
>> >> wrote:
>> >>
>> >>> Dear André,
>> >>>
>> >>> Thank you for your response.
>> >>> Could you send me such a script?
>> >>>
>> >>> On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura > >

Re: [gmx-users] The total charge is not integer : -0.00465

[SAKO MIRZAIE]

Dear Mark,

Thank you for your suggestion. That was true. I solved the problem.
Best,

On Fri, Dec 6, 2019 at 3:39 AM Mark Abraham 
wrote:

> Hi,
>
> If, for example, you inserted 465 polymer molecules each with charge -.001
> then the most appropriate path forward is to make the total charge of each
> molecule be neutral. But we don't know enough about what you're doing yet.
>
> Mark
>
> On Thu, 5 Dec 2019 at 23:34, SAKO MIRZAIE  wrote:
>
>> Dear Justin,
>>
>> Thank you for your answer. when I use just one chain of polymer with the
>> protein, the charge is an integer but when I employ "insert molecules" to
>> add more than one polymer chain, the charge will not be an integer. I am
>> wondering what's the problem?
>>
>> Best regards
>>
>> On Tue, Dec 3, 2019 at 4:04 PM Justin Lemkul  wrote:
>>
>> >
>> >
>> > On 12/3/19 3:59 PM, SAKO MIRZAIE wrote:
>> > > Hi All,
>> > > I did some MD  studies on a protein: polymer system. After running
>> > grompp,
>> > > it said, "the total charge is not an integer". the total charge is
>> > -0.00465.
>> > > Can I continue the MD by adding -maxwarn flag? or it will be a problem
>> > and
>> > > I will get unrealistic results?
>> >
>> > In general, it is never a good idea to use -maxwarn.
>> >
>> > The magnitude of that total charge is suspiciously high and you should
>> > check your topology for proper charge assignment.
>> >
>> > -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
>> >
>> > ==
>> >
>> >
>>
>> --
>> ***
>> Sako Mirzaie
>> Sako Mirzaie
>> Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
>> University of Sanandaj, Sanandaj, Iran
>>
>> Visiting Professor, Advanced Pharmaceutics
>>
>> & Drug Delivery Laboratory
>>
>> Leslie Dan Faculty of Pharmacy
>>
>> University of Toronto
>>
>> 144 College Street, Toronto, Ontario
>>
>> Canada M5S 3M2
>>
>> http://scholar.google.com/citations?user=viwZvVAJ=en
>>
>> http://www.scopus.com/authid/detail.url?authorId=54886431500
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
>> https://www.researchgate.net/profile/Sako_Mirzaie/publications/
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>

-- 
***
Sako Mirzaie
Sako Mirzaie
Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad
University of Sanandaj, Sanandaj, Iran

Visiting Professor, Advanced Pharmaceutics

& Drug Delivery Laboratory

Leslie Dan Faculty of Pharmacy

University of Toronto

144 College Street, Toronto, Ontario

Canada M5S 3M2

http://scholar.google.com/citations?user=viwZvVAJ=en

http://www.scopus.com/authid/detail.url?authorId=54886431500

http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie
https://www.researchgate.net/profile/Sako_Mirzaie/publications/
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[gmx-users] Regarding system shrunk

[Mijiddorj B]

Dear GMX users,

I study the interaction between polymer and surface interactions. Polymer
parameters were prepared by cgenff, and the parameters of the surface were
solved by INTERFACEFF. I performed short simulations, however, the system
was shrunk. I used the standard mdp file of charmm-gui membrane builder
excluding the smaller time steps and no-constraints.

If you have any experience, please advise me on how to solve this problem.

Best regards,

Mijiddorj
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[gmx-users] calculation of tilt angle of helix against the bilayer normal

[SHAHEE ISLAM]

hi,
i want to calculate the tilt angle of helix against the bilayer normal. iam
using this command
*gmx helixorient -s *.tpr -f *.xtc -n helix.ndx -oaxis -ocenter -orise
-oradius -otwist -obending -otilt -orot*
my question
1. how can i calculate the angle, so that angle can be calculated against
the bilayer normal.
2. by using this command i am able to analyse for 1 us coarse grained
simulation. But for the next 1 us run i am getting this error
 error too many iterations in routine jacobi
can anyone please guide me.
thanking you
shahee
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Re: [gmx-users] Chemical Shifts prediction using gmx chi -shift

[Florent Langenfeld]

Dear Christian,

Thanks for your answer.

Correct me if I'm wrong: the **-shift.dat grids contain chemical shift 
deviations compared to a set
of reference (amino-acid-dependent) chemical shifts (taken from table 2 of "D. 
S. Wishart and A. M. Nip, Protein
Chemical Shift Analysis: A Practical Guide, Biochem. Cell Biol., 76, 1998, 
153-163), and these deviations
are picked up according to the phi-psi angle of each residue (there are 18 rows 
and columns in the grid files,
so my guess is that dihedral angles are binned according to a 20° scheme), for 
each frame of the trajectory.

The final result is then the mean of the deviations for each chemical shift 
considered (Ca, Ha, CO and Cb).

In the paper you cite, I cannot find the reference value for Alanine and 
Tyrosine residues;
so I am wondering where the reference values for these residues come from.

Thanks again for your help!

Best,

Florent


Hello Florent,


The tool is based on? "D. S. Wishart and A. M. Nip", "Protein Chemical Shift Analysis: A 
Practical Guide", "Biochem.
Cell Biol.", 76, 1998, "153-163"

It reads chemical shift reference data on a phi-psi-angle grid from 
ca-shift.dat, cb-shift.dat, ha-shift.dat and
co-shift.dat. The tool interpolates this data for the respective angle and sums 
it up. This sum is then normalized by
the number of trajectory frames.


Best,

Christian


On 2019-12-06 17:39, Florent wrote:

Dear users,


I recently tried to use the -shift option of gmx chi, and I'm a bit confused 
about two things:

1) How does gromacs generate these results (chemical shift deviations from 
reference values)? The command-line
documentation is of little help ("Compute chemical shifts from phi/psi 
angles")...

2) What are the reference values for Alanine and Tyrosine residues from? The 
calculation generates a log with a
reference (Protein Chemical Shift Analysis: A Practical Guide), that does not 
contain any value for Alanine and
Tyrosine residues while chemical shifts deviations are computed for those 
residues...


Any help or reference to a more complete documentation would be appreciated.


Best,


Florent




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[gmx-users] Performance GROMACS on GPU

[Talarico Carmine]

Hi,
I run three simulations on 1 node with 3 GPU by using an increasing number of 
GPUs.

This is my system:
___
1 node with total 36 cores, 72 logical cores, 3 compatible GPUs

GROMACS version:2018.2
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:CUDA
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  hwloc-1.11.0
Tracing support:disabled
Built on:   2018-08-01 09:03:03

GPU info:
Number of GPUs detected: 3
#0: NVIDIA Tesla V100-PCIE-32GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#1: NVIDIA Tesla V100-PCIE-32GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
#2: NVIDIA Tesla V100-PCIE-32GB, compute cap.: 7.0, ECC: yes, stat: 
compatible
___

These are the launched commands on two different system size and related 
performances:

Command

ns/day

h/ns

Alchol Dehydrogenase system (95561 atoms)

gmx mdrun -deffnm topol -nb gpu -pme gpu -ntmpi 1 -ntomp 12

53.355

0.45

gmx mdrun -deffnm topol -nb gpu -pme gpu -ntmpi 2 -ntomp 12 -npme 1 -gputasks 01

53.176

0.451

gmx mdrun -deffnm topol -nb gpu -pme gpu -ntmpi 3 -ntomp 12 -npme 1 -gputasks 
012

50.024

0.48

Villin system (4723 atoms)

gmx mdrun -deffnm topol -nb gpu -pme gpu -ntmpi 1 -ntomp 12

589.635

0.041

gmx mdrun -deffnm topol -nb gpu -pme gpu -ntmpi 2 -ntomp 12 -npme 1 -gputasks 01

727.139

0.033

gmx mdrun -deffnm topol -nb gpu -pme gpu -ntmpi 3 -ntomp 12 -npme 1 -gputasks 
012

664.695

0.036


Despite the performances seems very strange, because by increasing the number 
of GPUs in a big system I can't seeing a speedup, while in a small system the 
performance's peak is reached with 2 GPU,
can I ask to all of you if I'm using the GPU's selection options in the right 
way?

Moreover, I'm not sure about the right usage of -ntomp option, I thought to ask 
in another session.

Thanks a lot!
Carmine

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Re: [gmx-users] (no subject)

[shakuntala dhurua]

Ok i will try, thank you so much

On Mon, 9 Dec 2019, 1:07 pm Tasneem Kausar, 
wrote:

> This problem also occurs in gromacs-5.1.4. Try higher version. We have done
> these calculations on gromacs-2016.
>
> On Mon, Dec 9, 2019 at 10:49 AM shakuntala dhurua <
> madhu.dhuru...@gmail.com>
> wrote:
>
> > here I am using gromacs version --- gromacs-5.1.5
> >
> > On Mon, Dec 9, 2019 at 10:43 AM Tasneem Kausar <
> tasneemkausa...@gmail.com>
> > wrote:
> >
> > > Please specify your gromacs version.
> > >
> > > On Mon, Dec 9, 2019 at 10:04 AM shakuntala dhurua <
> > > madhu.dhuru...@gmail.com>
> > > wrote:
> > >
> > > > hi
> > > > I am facing problem during hydrogen bond correlation c(t) with error
> > > > segmentation fault
> > > > I have used following flag for generate xtc file::- gmx trjconv -n
> > > > index.ndx -s ins_prod_1.tpr -f ins_prod_1.trr -o ins_prod_1.xtc -pbc
> > > > cluster
> > > > then for hydrogen bond correlation used following flag ::-gmx hbond
> -n
> > > > index.ndx -s ins_prod_1.tpr -f ins_prod_1.xtc -ac ins_prod_1.xvg
> > > > following error I am getting
> > > > Doing autocorrelation according to the theory of Luzar and Chandler.
> > > > Segmentation fault (core dumped)
> > > > please suggest me to solve this problem
> > > > --
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Re: [gmx-users] Chemical Shifts prediction using gmx chi -shift

[Christian Blau]

Hello Florent,


The tool is based on  "D. S. Wishart and A. M. Nip", "Protein Chemical Shift Analysis: A Practical Guide", "Biochem. 
Cell Biol.", 76, 1998, "153-163"


It reads chemical shift reference data on a phi-psi-angle grid from ca-shift.dat, cb-shift.dat, ha-shift.dat and 
co-shift.dat. The tool interpolates this data for the respective angle and sums it up. This sum is then normalized by 
the number of trajectory frames.



Best,

Christian


On 2019-12-06 17:39, Florent wrote:

Dear users,


I recently tried to use the -shift option of gmx chi, and I'm a bit confused 
about two things:

1) How does gromacs generate these results (chemical shift deviations from reference values)? The command-line 
documentation is of little help ("Compute chemical shifts from phi/psi angles")...


2) What are the reference values for Alanine and Tyrosine residues from? The calculation generates a log with a 
reference (Protein Chemical Shift Analysis: A Practical Guide), that does not contain any value for Alanine and 
Tyrosine residues while chemical shifts deviations are computed for those residues...



Any help or reference to a more complete documentation would be appreciated.


Best,


Florent


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