[gmx-users] Strange self-coefficient data with "-update gpu" option

[qing shao]

Hey,
We ran a quick simulation of a box of 884 spce water model using Gromacs
2020 on a workstation with an RTX 2080 card.
The water box was generated using gmx solvate command.
The whole simulation is 10 ns NPT + 10 ns NVT.
The self-diffusion coefficient is   D[OW] = 23.5350 (+/- 11.1866)
(1e-5 cm^2/s) if the MD simulation uses the "-update gpu" option
The value turns to normal as D[OW] = 2.5914 (+/- 0.0069) (1e-5
cm^2/s) without the "-update gpu" option.

Just wondering if anyone observed similar things.

Best,

Qing
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Re: [gmx-users] Regarding high RMSD

[Ashma Khan]

Thank for your suggestion Alessandra
I have applied the pbc conditions on my system in steps as follows:
1. gmx trjconv -f full_md.xtc -s full_md.tpr -pbc whole -o full_md_whole.xtc
2. gmx trjconv -f full_md_whole.xtc -s first_frame.gro -pbc nojump -o
full_md_nojump.xtc
3. gmx trjconv -f full_md_nojump.xtc -s full_md.tpr -pbc mol -ur compact
-center -o full_md_mol.xtc
After applying all these conditions, peptides of dimer diffusing out of the
box, both in opposite direction at the end of the simulation. kindly
suggest me what should I do.

-- 
Ashma Khan
Research Scholar
Department of Chemistry
AMU, Aligarh
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[gmx-users] Residue-Specific CMAPS in GROMACS

[Marcelo Depólo]

Hi all,

I've been investigating the implementation of CMAP in GROMACS and, as far
as I understood, the current CMAP format does not allow the use of
residue-specific CMAPS, since it is based on atomtypes and not on function
numbers, as GROMACS normally do.

For example, for AMBER, the function number '9' is defined for dihedral
format:
[ dihedrals ]
;  aiajakal funct
2 1 5 6 9

Considering that FFSB19 (
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.9b00591) uses
residue-specific CMAPs, it I create two different CMAPs for ALA and LEU
residues, it would lead to the same header format for both:

[ cmaptypes ]
C N CT C N 1 24 24\

Therefore, would it be possible to implement the use of function numbers
for CMAPs in GROMACS as well? That dummy '1' could be used as a CMAP ID and
called from the topology designed in .rtp file.

I am not expert in GROMACS code so I would appreciate any inputs that you
may find relevant.

Thanks in advance!
--
Marcelo Depolo Poleto
Postdoctoral Researcher
BIOAGRO - Room T07
Department of General Biology - UFV
Contact: + 55 31 3612-2464
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Re: [gmx-users] Troubleshooting Error Message: Invalid Index Group References

[Travis Meyer]

Thanks for your response! I checked and the cg_traj file contains atoms 
numbered 1-2000, which matches the atom IDs from the index file. The same 
trajectory does work using gmx angle with an angle index file created from the 
same python script which also includes atom IDs 1-2000 as well.
The fact that the error says "largest allowed atom index is 0" seems 
especially interesting to me, as it implies the gmx distance isn't finding any 
atoms in the trajectory file.
Travis Meyer, Ph.D.
INSPIRE Postdoctoral Fellow
Gormley Lab, Rutgers University
> Hello all,
>
> I am a brand new MD/GROMACS user, and I have been trying to learn how to
> use GROMACS for coarse-grained simulations using the MARTINI forcefield. I
> was going through a tutorial on coarse-graining from the MARTINI website (
> 
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcgmartini.nl%2Findex.php%2Ftutorials-general-introduction-gmx5%2Fmartini-tutorials-polymers-gmx5data=02%7C01%7Ctravis.meyer%40rutgers.edu%7Cf110fee0c56e442a988308d79b7a1aee%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C637148821067442954sdata=rBs2IvNHERRNN5IQbflOJCGJezD4jVHWREeFC2%2FMTuY%3Dreserved=0)
> but ran into an error I have been not been able to find a solution for.
>
> After coarse-graining the all-atom simulation to the COM between 3 atoms,
> I need to calculate bond lengths and angles in order to parameterize 
bonded
> interactions. Following instructions from the tutorial, I created index
> files for all bonds, angles, and dihedrals and used gmx distance along 
with
> the coarse-grained trajectory file. After choosing which index group I 
want
> to use, I receive an error message:
>

- Ignored:
> I am not familiar with the MARTINI tutorial, but I guess that the
particles numbers in your traj_cg are different from the one of
traj_allatoms.
Thus my suggestion is to check that the numbers reported in the index file
corresponds to the particles number that you have in your traj_cg.
The easy way to do it is to look  at  CG_gro file ( you can generate using
gmx traj in the same way that you have used for traj_cg

Best regards
Alessandra



> Inconsistency in user input: Invalid index group references encountered
> Group 'bonds_core1' cannot be used in selections, because it contains
> negative atom indices and/or references atoms not present (largest allowed
> atom index is 0).
>
> The index file itself contains all the proper atom indices. The fact that
> the error says "largest allowed atom index is 0" makes me think there is 
an
> error with my .xtc file, but I did not receive any errors when calculating
> angle distributions using the exact same trajectory file and appropriate
> angle index files.
>
> Are there any recommendations for how to go about fixing this?
>
> Thanks!

Travis Meyer, Ph.D.
INSPIRE Postdoctoral Fellow
Gormley Lab, Rutgers University
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Re: [gmx-users] gmx_topolbuild error (aayatt...@bose.res.in)

[Ray, Bruce D]

On Fri, 10 Jan 2020 11:15:36 +0530 (IST) , 
aayatt...@bose.res.in wrote:

Date: Fri, 10 Jan 2020 11:15:36 +0530 (IST)
From: aayatt...@bose.res.in
To: 
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] gmx_topolbuild error
Message-ID: 
<48026.103.230.166.2.1578635136.squir...@bose.res.in>
Content-Type: text/plain;charset=UTF-8

I am getting error in topolbuild:
Fatal error.
Source code file: readmol2.c, line: 693
Atom 1 (O5') has 2 connections when allowed 0
 I have used the command
./topolbuild -dir /home/aayatti/topolbuild1_2_1/dat/leap/parm -ff amber -n
tripos97
.mol2 file that I am using is as follows:
@MOLECULE
QCH
   3031 1 0 1
SMALL
USER_CHARGES
@ATOM
  1 O5'-1.9382342.2216390.669368 O 1 QCH
-0.6458 
  2 H5T-2.1610903.0855150.989879 H 1 QCH
0.4497 
  3 O3'-3.459429   -1.7287890.016186 O 1 QCH
-0.6852 
  4 H3T-3.700920   -2.3239170.713748 H 1 QCH
0.4392 
  5 C1'-0.662286   -0.787261   -0.296578 C 1 QCH
0.3964 
  6 H1'-0.605691   -1.741658   -0.791073 H 1 QCH
0.0394 
  7 C2'-1.435951   -0.8508841.016075 C 1 QCH
-0.0947 
  8 H2'1   -1.108767   -0.0641591.683744 H 1 QCH
0.0480 
  9 H2'2   -1.331556   -1.8073051.511592 H 1 QCH
0.0480 
 10 C3'-2.859368   -0.5759970.536996 C 1 QCH
0.2991 
 11 H3'-3.474441   -0.1270331.307751 H 1 QCH
0.0153 
 12 C4'-2.6446200.372686   -0.650794 C 1 QCH
0.1743 
 13 H4'-3.3101490.087545   -1.452894 H 1 QCH
0.0890 
 14 C5'-2.8289241.845500   -0.355885 C 1 QCH
0.0150 
 15 H5'1   -2.6332602.416008   -1.257986 H 1 QCH
0.0776 
 16 H5'2   -3.8587552.018514   -0.059368 H 1 QCH
0.0776 
 17 O4'-1.3046320.148647   -1.085285 O 1 QCH
-0.4154 
 18 N1  0.746765   -0.330172   -0.139522 N 1 QCH
-0.0020 
 19 C6  1.0374810.982281   -0.067547 C 1 QCH
-0.1180 
 20 H6  0.1890231.636860   -0.090671 H 1 QCH
0.2766 
 21 C5  2.3034181.4591660.033557 C 1 QCH
-0.2943 
 22 H5  2.5017892.5095650.085307 H 1 QCH
0.1984 
 23 C4  3.3551900.5215320.053970 C 1 QCH
0.4864 
 24 N4  4.6248250.8606340.131082 N 1 QCH
-0.8725 
 25 H41 5.3626320.1898710.139293 H 1 QCH
0.4651 
 26 H42 4.8875511.8213770.170549 H 1 QCH
0.4651 
 27 N3  3.028239   -0.778715   -0.004253 N 1 QCH
-0.2232 
 28 H3  3.730821   -1.4912290.018101 H 1 QCH
0.3215 
 29 C2  1.731998   -1.290150   -0.085103 C 1 QCH
0.4517 
 30 O2  1.543842   -2.458176   -0.098679 O 1 QCH
-0.4823 
@BOND
1 1 2 1
2 114 1
3 3 4 1
4 310 1
5 5 6 1
6 5 7 1
7 517 1
8 518 1
9 7 8 1
   10 7 9 1
   11 710 1
   121011 1
   131012 1
   141213 1
   151214 1
   161217 1
   171415 1
   181416 1
   191819 1
   201829 1
   211920 1
   221921 1
   232122 1
   242123 1
   252324 1
   262327 1
   272425 1
   282426 1
   292728 1
   302729 1
   312930 1
@SUBSTRUCTURE
  1  QCH  1    0   




kindly suggest to debug the error.
Thanking you in advance.


You do not have a properly formatted *.mol2 file.  It lacks proper
Tripos atom types in the sixth column.  In topolbuild, correct Tripos
atom types are critical for assignment of atom types in the final
gromacs topology.  I am surprised that this error message was triggered
rather than a message about not being able to find the atom types.  When
I get time now that I have been forced into retirement in my old age, I
hope to get back to refining this program, always provided that I am
able to remember what I did almost a decade ago.  In the meantime,
your oxygens and carbons need proper Tripos atom topology types.

 --
Bruce David Ray

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Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

[Justin Lemkul]

On 1/17/20 4:25 AM, András Ferenc WACHA wrote:

Dear Justin,

there are no name clashes in the .rtp files by design, I never re-use
already existing residue names. Beta3-homo-lysine is B3K,
beta2-homo-lysine is B2K, and disubstituted amino-acids also have their
naming scheme.


Sorry, no idea. This should work out of the box, because it's the normal 
behavior in force fields that have e.g. aminoacids.rtp, dna.rtp, etc. 
with matching .tdb files. Without access to the force field to dig into 
it, there's not much I can suggest other than putting everything into 
merged.rtp, merged.*.tdb, etc.


-Justin


Andras

On 1/16/20 11:34 PM, Justin Lemkul wrote:


On 1/16/20 10:07 AM, András Ferenc WACHA wrote:

Dear Justin,

thank you. Am I doing something wrong or is this a bug in Gromacs? Do
you have a suggestion how to make this work? Should I rename the
terminal patches or should I put everything under one basename
(sacrificing cleanliness and maintainability)?


Without spending a long time going through the code, likely what is
happening is pdb2gmx is loading the .rtp files in alphabetical order,
finding the first match of LYS (which occurs in your beta-amino acid
file) and loads the matching .tdb file - this is why alpha-amino acids
don't work; they're interpreted as beta. The cleanest solution would
probably be to prefix your beta-amino acids to change their residue
names, e.g. BLYS instead of LYS in both the .rtp and coordinate files.

-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] com motion and position restraints may cause artifacts

[Justin Lemkul]

On 1/17/20 3:01 AM, Berk Hess wrote:

Hi,

Using center of mass motion removal in combination with an absolute reference 
in the system, such as position restraints, will always lead to artifacts, as 
physical motion is removed and not drift due to numerical rounding errors. For 
the most common case of equilibrating macromolecules using position restraints 
these artifacts are usually negligible.

So we should probably add a sentence to the note:
Removing center of mass motion in the presence of positions restraints  might 
cause artifacts. When position restraints are used to equilibrate a 
macromolecule these artifacts are usually negligible.


Thanks, Berk. I do think this addition would be important. Most people 
are going to encounter the note doing exactly what you describe, 
equilibrating a macromolecule. If the artifacts are negligible in this 
case, it should be made clear to avoid concern.


-Justin


I think we should add a comm-removal setting "auto" which should be the 
default, so grompp can automatically turn off comm-removal when using position restraints.

I realize now that we should check if there are no other artifacts when doing 
equilibration with position restraints in an NPT ensemble without comm-removal. 
I expect NVT should be fine without comm-removal.

Cheers,

Berk


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Christos Deligkaris 

Sent: Thursday, January 16, 2020 5:03 PM
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] com motion and position restraints may cause artifacts

The ambiguity in the gromacs 2020 note made me concerned, as it was
not clear to me whether my system (DNA+small molecule) fills in the
category where artifacts are caused. The gromacs note could have been
a bit more helpful by referencing specific publications so that we can
educate ourselves.

Best wishes,

Christos Deligkaris, PhD

On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul  wrote:



On 1/16/20 5:17 AM, Alessandra Villa wrote:

Hi,

On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris 
wrote:


dear all,

I installed gromacs 2020 and I now get the following message during
equilibration:

NOTE 1 [file nvt.mdp]:

Removing center of mass motion in the presence of position
restraints  might cause artifacts

I do not recall seeing this with gromacs 2018. In which cases are
artifacts created? Is it now recommended to not remove the center of
mass motion during equilibration?



It is recommended not to have position restrain and remove of center of
mass at the same moment. That is also the case of the equilibration phase.
That may cause artifact depending on the system and the condition you are
simulating.

What is the nature of these artifacts and where is this documented?
Combining position restraints with COM motion removal is an extremely
common practice. Phrases like "might cause artifacts" are troubling
because that implies uncertainty. Are there cases when this combination
does not cause artifacts?

-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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--
==

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] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[Justin Lemkul]

On 1/17/20 7:12 AM, ZHANG Cheng wrote:

Many thanks for Justin's advice forassigning the same number of PP and PME ranks in 
each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not familiar with these kind of 
settings, can I ask how to do this exactly? e.g. how to change "gmx mdrun -deffnm md_0_1 
-cpi -append" ?



As Quyen noted, you're simulating different systems with each version. 
You can't do that and expect to establish a benchmark. Run the exact 
same input in both versions to establish how well each performs.


If you want to tweak performance settings, refer to the manual and 
consult gmx help mdrun.


-Justin




--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Fri, Jan 17, 2020 00:57 AM
To:"gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200116



The MD is run on our HPC cluster. So I personally could not compile it. Is 
there still some way to get equivalent performance for the Version 2019?




-- Original --
From:"ZHANG Cheng"<272699...@qq.com;
Date:Thu, Jan 16, 2020 07:58 AM
To:"ZHANG 
Cheng"<272699...@qq.com;"gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200115;?


Thank you!


-- Original --
From:"ZHANG Cheng"<272699...@qq.com;
Date:Thu, Jan 16, 2020 03:38 AM
To:"gromacs.org_gmx-users"http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce 
-inter -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL 
-nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append


--
==

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] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[ZHANG Cheng]

Many thanks for Justin's advice forassigning the same number of PP and 
PME ranks in each run (30/6 in 5.1.1 and 27/9 in 2019.3). Sorry I am not 
familiar with these kind of settings, can I ask how to do this exactly? e.g. 
how to change "gmx mdrun -deffnm md_0_1 -cpi -append" ?




--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Fri, Jan 17, 2020 00:57 AM
To:"gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200116



The MD is run on our HPC cluster. So I personally could not compile it. Is 
there still some way to get equivalent performance for the Version 2019?




-- Original --
From:"ZHANG Cheng"<272699...@qq.com;
Date:Thu, Jan 16, 2020 07:58 AM
To:"ZHANG 
Cheng"<272699...@qq.com;"gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200115;?


Thank you!


-- Original --
From:"ZHANG Cheng"<272699...@qq.com;
Date:Thu, Jan 16, 2020 03:38 AM
To:"gromacs.org_gmx-users"http://www.mdtutorials.com/gmx/lysozyme/index.html
The commands I used are listed below.


gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce 
-inter -ignh -merge interactive
gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p topol.top
gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn 1 
gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA -nname CL 
-nn 31 -neutral -conc 0.05
(Afterwards, using the HPC to run)
gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
gerun mdrun_mpi -v -deffnm em
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gerun mdrun_mpi -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gerun mdrun_mpi -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
gmx mdrun -deffnm md_0_1 -cpi -append
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Re: [gmx-users] Why it is run so slow in gromacs 2019.3 compared to VERSION 5.1.1?

[Quyen V. Vu]

He said he ran a nearly identical simulation on two versions of gromacs but
I didn't think so,
in 2019.3 logs:

There are: 117860 Atoms
Atom distribution over 27 domains: av 4365 stddev 75 min 4289 max 4626
and 5.1 logs:
There are: 127790 Atoms
Atom distribution over 30 domains: av 4259 stddev 90 min 4193 max 4370

On Thu, Jan 16, 2020 at 11:37 PM Justin Lemkul  wrote:

>
>
> On 1/16/20 11:57 AM, ZHANG Cheng wrote:
> > I have re-run the MD, with only 2 ps in both version. Indeed, the
> Version 2019 is far slower than the Version 5.1.1.
> >
> >
> > Version 2019 needs 114.111 hours to complete 1 ns, while Version 5.1.1
> only needs6.362 hours to complete 1 ns.
> >
> >
> > The new logs files are at
> > https://github.com/lanselibai/gromacs-20200116
> >
> >
> >
> > The MD is run on our HPC cluster. So I personally could not compile it.
> Is there still some way to get equivalent performance for the Version 2019?
> >
>
> Try assigning the same number of PP and PME ranks in each run (30/6 in
> 5.1.1 and 27/9 in 2019.3). You're losing a lot of performance in
> communicating PME forces in the 2019.3 run. You may also want to try
> version 2020 to see if automatic detection has improved.
>
> -Justin
>
> >
> >
> > --Original--
> > From:"ZHANG Cheng"<272699...@qq.com;
> > Date:Thu, Jan 16, 2020 07:58 AM
> > To:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"<
> gromacs.org_gmx-users@maillist.sys.kth.se;
> >
> > Subject:Re:Why it is run so slow in gromacs 2019.3 compared to
> VERSION 5.1.1?
> >
> >
> >
> > Hi Justin, what kind of information should I look at in the log files?
> They are too big to paste here. Would it be possible if you can see them at
> https://github.com/lanselibai/gromacs-20200115;?
> >
> >
> > Thank you!
> >
> >
> > -- Original --
> > From:"ZHANG Cheng"<272699...@qq.com;
> > Date:Thu, Jan 16, 2020 03:38 AM
> > To:"gromacs.org_gmx-users"<
> gromacs.org_gmx-users@maillist.sys.kth.se;
> > Cc:"ZHANG Cheng"<272699...@qq.com;
> > Subject:Why it is run so slow in gromacs 2019.3 compared to
> VERSION 5.1.1?
> >
> >
> >
> > I have a nearly identical run using the "VERSION 2019.3" compared to my
> previous "VERSION 5.1.1". Everything during the preparation is the same
> except "-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r
> nvt.gro" and "-r npt.gro" are added in the grompp commands for NVT, NPT and
> production run, respectively.
> >
> >
> > Using "-pe mpi 12" (i.e. 12 nodes) per hour, only 5-7 ps can be
> processed in the "VERSION 2019.3", while 200 ps can be achieved in the
> "VERSION 5.1.1". Can I ask is this normal? Is there some configuration I
> can do in the "VERSION 2019.3" so as to accelerate the MD?
> >
> >
> > I follow Justin's tutorial at
> http://www.mdtutorials.com/gmx/lysozyme/index.html
> > The commands I used are listed below.
> >
> >
> > gmx pdb2gmx -f Fab.pdb -o Fab_processed.gro -water spce
> -inter -ignh -merge interactive
> > gmx editconf -f Fab_processed.gro -o Fab_newbox.gro -c -d 1.0 -bt cubic
> > gmx solvate -cp Fab_newbox.gro -cs spc216.gro -o Fab_solv.gro -p
> topol.top
> > gmx grompp -f ions.mdp -c Fab_solv.gro -p topol.top -o ions.tpr -maxwarn
> 1
> > gmx genion -s ions.tpr -o Fab_solv_ions.gro -p topol.top -pname NA
> -nname CL -nn 31 -neutral -conc 0.05
> > (Afterwards, using the HPC to run)
> > gmx grompp -f minim.mdp -c Fab_solv_ions.gro -p topol.top -o em.tpr
> > gerun mdrun_mpi -v -deffnm em
> > gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
> > gerun mdrun_mpi -deffnm nvt
> > gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r
> nvt.gro
> > gerun mdrun_mpi -deffnm npt
> > gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r
> npt.gro
> > gmx mdrun -deffnm md_0_1 -cpi -append
>
> --
> ==
>
> 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] Ran into trouble installing Gromacs API

[Marko Petrovic]

Hello

I have (I think successfully) installed Gromacs 2020 on my computer (MacOS X 
Catalina) and tried to install the API using the quick install guide: 
https://gmxapi.readthedocs.io/en/latest/quickstart.html
and get stuck on the step:

pip install -r requirements.txt

as that file does not seem to be in that folder of the repo. I found the file 
"requirements-test.txt" in the folder "python-packaging" and tried with that 
but got a long error message of missing stuff I didn't understand, I'm hoping 
those error messages are from the file not being intended for use inn the 
manner I tried so I'm currently not including those here.

Should I have installed gromacs 2019 for which the API was developed? Has 
anyone else installed the API recently and (hopefully) exxperienced and 
overcome this hurdle?

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

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Re: [gmx-users] pdb2gmx picks up the wrong .tdb files?

[András Ferenc WACHA]

Dear Justin,

there are no name clashes in the .rtp files by design, I never re-use
already existing residue names. Beta3-homo-lysine is B3K,
beta2-homo-lysine is B2K, and disubstituted amino-acids also have their
naming scheme.

Andras

On 1/16/20 11:34 PM, Justin Lemkul wrote:
>
>
> On 1/16/20 10:07 AM, András Ferenc WACHA wrote:
>>
>> Dear Justin,
>>
>> thank you. Am I doing something wrong or is this a bug in Gromacs? Do
>> you have a suggestion how to make this work? Should I rename the
>> terminal patches or should I put everything under one basename
>> (sacrificing cleanliness and maintainability)?
>>
>
> Without spending a long time going through the code, likely what is
> happening is pdb2gmx is loading the .rtp files in alphabetical order,
> finding the first match of LYS (which occurs in your beta-amino acid
> file) and loads the matching .tdb file - this is why alpha-amino acids
> don't work; they're interpreted as beta. The cleanest solution would
> probably be to prefix your beta-amino acids to change their residue
> names, e.g. BLYS instead of LYS in both the .rtp and coordinate files.
>
> -Justin
>
-- 
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] cluster analysis_group selection

[Jin Zhang]

Hi,

Hope this helps:
https://ctlee.github.io/BioChemCoRe-2018/clustering/
In case you may want to align the trajectory using one group but calculate
RMSD using another group, you can choose no fit when doing clustering. In
that case, gmx trajconv can be used before doing clustering.

Best,
Jin
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Re: [gmx-users] Problem while running equilibration

[Alessandra Villa]

Hi,
see some comments/suggestions below.
Best regards
Alessandra

On Fri, Jan 17, 2020 at 8:34 AM Nirali Desai 
wrote:

> Dear all,
>
> My system consists of a three chains of protein: PROA, PROB and PROCLIG
> (with ligand).
> Minimization is running properly without any error.
> Parameters used are:
> title = Minimization ; Title of run
> define  = -DPOSRES
>
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep ; Algorithm (steep = steepest descent minimization)
> emtol = 1000   ; Stop minimization when the maximum force < 10.0 kJ/mol
> emstep  = 0.01  ; Energy step size
> nsteps = 5   ; Maximum number of (minimization) steps to perform
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
> freezegrps  = PROCLIG
> freezedim   = Y Y Y
>
> But, while running equilibration it is giving error of the blowing up of
> the system like water molecule not settled, clashes etc.
> I ran the equilibration without adding water and also without using freeze
> groups. It is running perfectly. I turned off constraints and pressure
> coupling while using freezegroups.
>  Parameters used:
>
> title   = Protein-ligand complex NVT equilibration
> define  = -DPOSRES  ; position restrain the protein and ligand
>


> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 5 ; 2 * 5 = 100 ps
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 100   ; save coordinates every 0.2 ps
> nstvout = 100   ; save velocities every 0.2 ps
> nstenergy   = 100   ; save energies every 0.2 ps
> nstlog  = 100   ; update log file every 0.2 ps
> energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
> energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
> SOL
>

Why do you use energygrp_excl ?   Usually  energygrp_excl are useful for
speeding up energy calculations with mdrun -rerun and for excluding
interactions within frozen groups (in your case only PROCLIG)

freezegrps  = PROCLIG
> freezedim   = Y Y Y
>

Do you need to freeze group?
You already have position restrains on protein and ligand



> ; Bond parameters
> continuation= no; first dynamics run
> constraints = none ; all bonds (even heavy atom-H bonds)
> constrained
>

You are using 2fs and atomistic force field, then you need at least h-bond
to be constrained



> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> cutoff-scheme  = group
> nstlist = 20 ; 10 fs
> rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
> rvdw= 0.9   ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling
> tcoupl  = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein non-protein   ; two coupling groups - more accurate
> tau_t   = 0.1   0.1 ; time constant, in ps
> ref_t   = 300   300 ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl  = no; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes   ; assign velocities from Maxwell distribution
> gen_temp= 300   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
>
> Please guide me on this.
> If you have any suggestions I will really appreciate.
>
> Thanks and regards,
> Nirali
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Re: [gmx-users] Regarding high RMSD

[Alessandra Villa]

Hi,

On Fri, Jan 17, 2020 at 6:39 AM Ashma Khan  wrote:

> Thank you for your suggestion Alessandra Villa
> I have applied all types of pbc conditions but my one peptide is diffusing
> away from another peptide in case of dimer after half of the simulation
> time and rmsd is coming out 100 Angstrom after that time which is very
> high. Please suggest me what should I do.
>

When you visualize the trajectory (for example in VMD), you see the dimer
breaking and the two peptides moving apart inside the box
(in a "continuous" way and not jumping in and out the box or moving out of
the box).
That probably means that in your simulation condition, the two peptides do
not form a dimer.

Best regards
Alessandra





> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
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Re: [gmx-users] com motion and position restraints may cause artifacts

[Berk Hess]

Hi,

Using center of mass motion removal in combination with an absolute reference 
in the system, such as position restraints, will always lead to artifacts, as 
physical motion is removed and not drift due to numerical rounding errors. For 
the most common case of equilibrating macromolecules using position restraints 
these artifacts are usually negligible.

So we should probably add a sentence to the note:
Removing center of mass motion in the presence of positions restraints  might 
cause artifacts. When position restraints are used to equilibrate a 
macromolecule these artifacts are usually negligible.

I think we should add a comm-removal setting "auto" which should be the 
default, so grompp can automatically turn off comm-removal when using position 
restraints.

I realize now that we should check if there are no other artifacts when doing 
equilibration with position restraints in an NPT ensemble without comm-removal. 
I expect NVT should be fine without comm-removal.

Cheers,

Berk


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Christos 
Deligkaris 
Sent: Thursday, January 16, 2020 5:03 PM
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] com motion and position restraints may cause artifacts

The ambiguity in the gromacs 2020 note made me concerned, as it was
not clear to me whether my system (DNA+small molecule) fills in the
category where artifacts are caused. The gromacs note could have been
a bit more helpful by referencing specific publications so that we can
educate ourselves.

Best wishes,

Christos Deligkaris, PhD

On Thu, Jan 16, 2020 at 5:21 AM Justin Lemkul  wrote:
>
>
>
> On 1/16/20 5:17 AM, Alessandra Villa wrote:
> > Hi,
> >
> > On Mon, Jan 13, 2020 at 3:36 PM Christos Deligkaris 
> > wrote:
> >
> >> dear all,
> >>
> >> I installed gromacs 2020 and I now get the following message during
> >> equilibration:
> >>
> >> NOTE 1 [file nvt.mdp]:
> >>
> >>Removing center of mass motion in the presence of position
> >> restraints  might cause artifacts
> >>
> >> I do not recall seeing this with gromacs 2018. In which cases are
> >> artifacts created? Is it now recommended to not remove the center of
> >> mass motion during equilibration?
> >>
> >>
> > It is recommended not to have position restrain and remove of center of
> > mass at the same moment. That is also the case of the equilibration phase.
> > That may cause artifact depending on the system and the condition you are
> > simulating.
>
> What is the nature of these artifacts and where is this documented?
> Combining position restraints with COM motion removal is an extremely
> common practice. Phrases like "might cause artifacts" are troubling
> because that implies uncertainty. Are there cases when this combination
> does not cause artifacts?
>
> -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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