Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

[Guyen Gn]

Any ideas on this one? Thanks!

On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn  wrote:

> Still did not work. change xMIC to xCore and log is below (if it was other
> way around, then originally it must have not worked).
> Script file is all oneline.
>
> -- Performing Test C_xCORE_AVX512_FLAG_WORKS
> -- Performing Test C_xCORE_AVX512_FLAG_WORKS - Failed
> -- Performing Test C_mavx512f_mfma_FLAG_WORKS
> -- Performing Test C_mavx512f_mfma_FLAG_WORKS - Failed
> -- Performing Test C_mavx512f_FLAG_WORKS
> -- Performing Test C_mavx512f_FLAG_WORKS - Failed
> -- Performing Test C_arch_AVX_FLAG_WORKS
> -- Performing Test C_arch_AVX_FLAG_WORKS - Failed
> -- Performing Test C_hgnu_FLAG_WORKS
> -- Performing Test C_hgnu_FLAG_WORKS - Failed
> -- Performing Test C_FLAG_WORKS
> -- Performing Test C_FLAG_WORKS - Success
> -- Performing Test C_COMPILE_WORKS
> -- Performing Test C_COMPILE_WORKS - Failed
> -- Compiler flag was valid, but executable did not build - perhaps update
> the binutils package
> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS
> -- Performing Test CXX_xCORE_AVX512_FLAG_WORKS - Failed
> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS
> -- Performing Test CXX_mavx512f_mfma_FLAG_WORKS - Failed
> -- Performing Test CXX_mavx512f_FLAG_WORKS
> -- Performing Test CXX_mavx512f_FLAG_WORKS - Failed
> -- Performing Test CXX_arch_AVX_FLAG_WORKS
> -- Performing Test CXX_arch_AVX_FLAG_WORKS - Failed
> -- Performing Test CXX_hgnu_FLAG_WORKS
> -- Performing Test CXX_hgnu_FLAG_WORKS - Failed
> -- Performing Test CXX_FLAG_WORKS
> -- Performing Test CXX_FLAG_WORKS - Success
> -- Performing Test CXX_COMPILE_WORKS
> -- Performing Test CXX_COMPILE_WORKS - Failed
> -- Compiler flag was valid, but executable did not build - perhaps update
> the binutils package
> CMake Error at cmake/gmxManageSimd.cmake:92 (message):
>   Found a compiler flag for AVX 512F support, but some other problem
> exists.
>   Update your assembler and/or linker, e.g.  in the binutils package of
> your
>   distribution.
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:314 (gmx_give_fatal_error_when_
> simd_support_not_found)
>   CMakeLists.txt:666 (gmx_manage_simd)
>
>
> -- Configuring incomplete, errors occurred!
>
>
> On Mon, Jul 3, 2017 at 2:44 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> On Mon, Jul 3, 2017 at 10:50 PM Guyen Gn  wrote:
>>
>> > Sorry for long wait on response, basically i followed the instruction at
>> > nvidia website:
>> >
>> > http://www.nvidia.com/object/gromacs-installation.html
>> >
>> > I instaled GPU driver versoin 369, as well as CUDA, gcc, cmake. After
>> that
>> > it tells to run following:
>> >
>> > CC=gcc CXX=g++ cmake  -DGMX_OPENMP=ON -DGMX_GPU=ON -
>> > DGPU_DEPLOYMENT_KIT_ROOT_DIR= -DGMX_BUILD_OWN_FFTW=ON -
>> > DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_BUILD_TYPE=Release -
>> > DCMAKE_INSTALL_PREFIX=
>> >
>> > I tweaked as follows to fit my environment I setup (basically just
>> > installation source and run directory:
>> > CC=gcc CXX=g++ cmake /root/gromacs/gromacs-2016 -DGMX_OPENMP=ON
>> > -DGMX_GPU=ON -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda
>> > -DGMX_BUILD_OWN_FFTW=ON -DGMX_PREFER_STATIC_LIBS=ON
>> > -DCMAKE_BUILD_TYPE=Release
>> > -DCMAKE_INSTALL_PREFIX=/root/gromacs/gromacs-2016-run inside build.sh
>> shell
>> > script.
>> >
>> > This is the full log, I highlighted toward the end section of code
>> where it
>> > started to fail. It appears something related to AVX. Thanks.,
>> >
>> > [root@localhost gromacs-2016]# ./build.sh
>> > CMake Error: The source directory "/root/gromacs/gromacs-2016/-" does
>> not
>> > exist.
>> > Specify --help for usage, or press the help button on the CMake GUI.
>> > ./build.sh: line 2: -DGMX_BUILD_OWN_FFTW=ON: command not found
>> > ./build.sh: line 3: -DCMAKE_BUILD_TYPE=Release: command not found
>> >
>>
>> All the above is because your script needed editing to handle newlines
>> from
>> your copy-paste.
>>
>>
>> > [root@localhost gromacs-2016]# nano -w build.sh
>> > [root@localhost gromacs-2016]# pwd
>> > /root/gromacs/gromacs-2016
>> > [root@localhost gromacs-2016]# mkdir ~/gromacs/gromacs-run
>> > [root@localhost gromacs-2016]# ./build.sh
>> > -- The C compiler identification is GNU 4.8.5
>> > -- The CXX compiler identification is GNU 4.8.5
>> > -- Check for working C compiler: /usr/bin/gcc
>> > -- Check for working C compiler: /usr/bin/gcc -- works
>> > -- Detecting C compiler ABI info
>> > -- Detecting C compiler ABI info - done
>> > -- Check for working CXX compiler: /usr/bin/g++
>> > -- Check for working CXX compiler: /usr/bin/g++ -- works
>> > -- Detecting CXX compiler ABI info
>> > -- Detecting CXX compiler ABI info - done
>> > -- Performing Test CXXFLAG_STD_CXX0X
>> > -- Performing Test CXXFLAG_STD_CXX0X - Success
>> > -- Performing Test CXX11_SUPPORTED
>> > -- Performing Test CXX11_SUPPORTED - Success
>> > -- Performing Test CXX11_STDLIB_PRESENT
>> > -- Performing Test CXX11_STDLIB_PRESENT - 

Re: [gmx-users] NPT problem

[Alex]

No, I mean that:

1. Graphene dimensions cannot be exactly 9 x 9. It is a crystal and its
in-plane dimensions are _precisely_ determined by the unit cell counts in
the corresponding directions.
2. The box size needs to be adjusted in accordance with basic geometry of
the crystal and its lattice orientation relative to the rectangular box.
3. With a difference of 2 nm between box size and sample dimensions, there
is no way your PBC  request is properly processed by x2top. You are likely
obtaining a finite sheet instead of a self-passivated periodic sheet and
then edges are causing issues.
4. Until you make some effort to learn about graphene and crystals (prior
to solvating and doing other things), nothing will work and noone here will
be able to help.

Alex

On Fri, Jul 14, 2017 at 1:09 AM,  wrote:

> The graphene is 9*9 nm, and I proposed the box to be 11*11 nm. Do you mean
> that the box dimensions are small and thats the problem?
> Thanks,Mohammad
>   From: Alex 
>  To: Discussion list for GROMACS users ;
> Discussion list for GROMACS users 
>  Sent: Friday, 14 July 2017, 11:31:06
>  Subject: Re: [gmx-users] NPT problem
>
>
> >
> > I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT
> > -noparam -pbc" for generating the topology. then I used "gmx editconf
> > -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating
> > the box
> >
> And where did "-box 11 11 11" come from? For pbc to work the box in your
> case has to be a certain size corresponding to the graphene dimensions.
> And no, it is not simply its approximate X-Y dimensions.
>
> Alex
>
> >
> > 
> > *From:* Alex 
> > *To:* Discussion list for GROMACS users ;
> > Mohammad Roostaie 
> > *Sent:* Thursday, 13 July 2017, 22:51:48
> > *Subject:* Re: [gmx-users] NPT problem
> >
> > Also, that tutorial's parameters that are completely wrong for
> > graphene. For bulk graphene bond types I suggest:
> >
> > CJCJ  10.14200  420420.0
> >
> > For bulk angles:
> >
> > CJCJCJ  1  120.000659.346
> >
> > For bulk dihedrals:
> >
> >  CJCJCJCJ  3 17.30770  0.0 -17.30770
> > 0.0 0.0  0.0
> >
> > These are parameters obtained from a Taylor-expanded optimized
> > Tersoff-Brenner potential. Please count the number of bonds and
> > dihedrals in your graphene model, as produced by x2top. If the number
> > of dihedrals divided by the number of bonds gives you a number, say,
> > equal to m, then multiply the dihedral parameters by that number. And
> > do NOT use bond constraints -- you are simulating a crystal.
> >
> > Alex
> >
> > On Thu, Jul 13, 2017 at 10:45 AM,  > > wrote:
> >
> >Hi All GROMACS users,
> >
> >
> >
> >I created graphene with nanotube modeler then I created a force
> >field for graphene based on OPLS (by using this link and its
> >parameters: http://chembytes.wikidot.com/ grocnt
> >). I generated the topology
> >file using x2top command. I put the graphene inside a box of water
> >(TIP3P) which was larger than the graphene dimension with 1000
> >  (kJ/mol nm^2) position restraint on all the atoms, and I
> >performed the energy minimization and NVT equilibrations (in order
> >to get an optimized structure of the graphene for further
> >simulations). The results of both of them were good (energy level
> >has reached a negative value with the order of 6 and the
> >temperature has converged the preferred value). But, when I run
> >the NPT equilibration, the results are not good (the pressure and
> >density fluctuated very much and the averaged values are so far
> >from the preferred ones). Also, during the NPT run, I received
> >these messages:
> >
> >
> >step 53965: Water molecule starting at atom 127424 can not be settled.
> >
> >Check for bad contacts and/or reduce the timestep if appropriate.
> >
> >Wrote pdb files with previous and current coordinates
> >
> >
> >
> >step 141454: Water molecule starting at atom 53366 can not be settled.
> >
> >Check for bad contacts and/or reduce the timestep if appropriate.
> >
> >Wrote pdb files with previous and current coordinates
> >
> >
> >
> >step 141483: Water molecule starting at atom 53366 can not be settled.
> >
> >Check for bad contacts and/or reduce the timestep if appropriate.
> >
> >Wrote pdb files with previous and current coordinates
> >
> >
> >
> >step 323815: Water molecule starting at atom 30509 can not be settled.
> >
> >Check for bad contacts and/or reduce the timestep if appropriate.
> >
> >Wrote pdb files with previous and current coordinates
> >
> >
> >
> >step 

Re: [gmx-users] Scd or -Scd?

[Thomas Piggot]

That should have read |Scd| and not [Scd] in the last sentence.

On 14/07/17 18:40, Thomas Piggot wrote:
As far as I'm aware (and happy to be corrected if someone knows 
better) it is simply a convention that stems from the fact that the 
signs of the order parameters were not originally determined from 
experiments and so were reported in these works as |Scd|. Given that 
the order parameters of the lipid tails are pretty much always 
negative, it makes sense to show -Scd to keep the plots looking the 
same as those that report the absolute values of the Scd.


That said, you should be careful with reporting the absolute values 
though as the order parameters (Scd) can theoretically vary between 
-0.5 and 1. Indeed with some force fields (e.g. ones with unsaturated 
double bonds) you can have order parameters that do cross 0 (i.e. will 
be plotted incorrectly if you report [Scd]).


Cheers

Tom (not Justine!)

On 14/07/17 18:01, m g wrote:
Dear Justine,Why are the order parameter data reported in articles as 
-S_CD (minus S_CD)?

Thanks,Ganj




--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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Re: [gmx-users] Scd or -Scd?

[Thomas Piggot]

As far as I'm aware (and happy to be corrected if someone knows better) 
it is simply a convention that stems from the fact that the signs of the 
order parameters were not originally determined from experiments and so 
were reported in these works as |Scd|. Given that the order parameters 
of the lipid tails are pretty much always negative, it makes sense to 
show -Scd to keep the plots looking the same as those that report the 
absolute values of the Scd.


That said, you should be careful with reporting the absolute values 
though as the order parameters (Scd) can theoretically vary between -0.5 
and 1. Indeed with some force fields (e.g. ones with unsaturated double 
bonds) you can have order parameters that do cross 0 (i.e. will be 
plotted incorrectly if you report [Scd]).


Cheers

Tom (not Justine!)

On 14/07/17 18:01, m g wrote:

Dear Justine,Why are the order parameter data reported in articles as -S_CD 
(minus S_CD)?
Thanks,Ganj


--
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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[gmx-users] Scd or -Scd?

[m g]

Dear Justine,Why are the order parameter data reported in articles as -S_CD 
(minus S_CD)? 
Thanks,Ganj
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[gmx-users] (no subject)

[Jivesh Madan]

jivesh.mad...@gmail.com
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[gmx-users] 'fudgeQQ' parameter in the topology file

[Sara Del Galdo]

Dear Gromacs user,

I read from the Gromacs Manual (version 5.1.2) that, while fudgeLJ is used
only when
generate pairs is set to ‘yes’, fudgeQQ is always used.

1. If I set  fudgeQQ = 0.0, will gromacs annulate the 1-4 interactions ?

2. If I explicitly insert a (Coulomb 1-4) scaling factor in my [pairs]
section in the topology file, will Gromacs use both the scaling factor and
fudgeQQ ?
For example, how Gromacs will manage the following case (where the 4-th
coloumn in my pairs section is the scaling factor mentioned above)?

 [ defaults ]
; nbfunc   comb-rule   gen-pairs  fudgeLJ  fudgeQQ
 1   2  no   0.5 0.8333
[ pairs ]
; 1-4 interactions
  1   8   20.833   -0.5360.1150.2875 0.14940
  1   9   20.833   -0.5360.1170.2875 0.14940
  1  10   20.833   -0.536   -0.0330.3400 0.22821
  1  23   20.833   -0.536   -0.3270.3105 0.39527
  :  :   :::::  :


Thanks in advance.
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[gmx-users] equilibration

[‪farial tavakoli‬ ‪]

Hi justin
 Thank you for reply and sorry for sending in another email, because when i 
wanted to reply, it was rejected.Actually, since i am a new gromacs user, i 
used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 
4 ) tuturial in gromacs. And did all the steps and issued all commands that 
said in this tuturial . I also generated my ligand topology by PRODRG and 
edited the charges and charge groups . To edit atome charge, according to 
aminoacids.rtp file, i considered what my atomes are bonded to , in order to 
best give their charge. Then , regarding to the article : Practical 
considerations for building GROMOS-compatible small-molecule topologiesEditted 
the charge groups , but i think , maybe i was wrong in specifying charg groups. 
In addition, i noticed that there was a wrong bond in the gromacs topology ang 
gromacs cordinate files, so i corrected them but i dont know if i did right?  
These are all that i did. I dont know more about generating ligand topology but 
informatin that said in this tuturial. If you let me, send my ligand topology 
file to you? 
With best regardsFarial
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Re: [gmx-users] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi justin
 Thank you for replyActually, since i am a new gromacs user, i used all .mdp 
files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial 
in gromacs. And did all the steps and issued all commands that said in this 
tuturial . I also generated my ligand topology by PRODRG and edited the charges 
and charge groups . To edit atome charge, according to aminoacids.rtp file, i 
considered what my atomes are bonded to , in order to best give their charge. 
Then , regarding to the article : Practical considerations for building 
GROMOS-compatible small-molecule topologiesEditted the charge groups , but i 
think , maybe i was wrong in specifying charg groups. In addition, i noticed 
that there was a wrong bond in the gromacs topology ang gromacs cordinate 
files, so i corrected them but i dont know if i did right?  These are all that 
i did. I dont know more about generating ligand topology but informatin that 
said in this tuturial. If you let me, send my ligand topology file to you? 
With best regardsFarial

Sent from Yahoo Mail for iPhone


On Friday, July 14, 2017, 2:59 PM, Justin Lemkul  wrote:



On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi Justin
> Thank you so much for your reply about minimize ligand in vacuoaccording to 
> :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
>( one or more water molecules can not to be settled . check for bad contacts 
>or reduce time step))I checked my protein in desired solvent as i noticed in 
>the previous mail, and it was stable. i minimized my ligand too in vacuo with 
>the .mdp file which you advised me, it was minimized well and monitored by 
>pymol, its configuration was ok.
> In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
> error in 2 steps.then, reduced the temperature to 100 k , but the same error 
> displayed again.
> Actually, I cant understand some advices and causes in this site. like:
> I dont understand  some of causes and advices in this site, include:1) you 
> are doing particle insertion in free energy calculations without using soft 
> core2) your position restraints are to coordinates too different from those 
> present in the system3) Make sure the forces don't get that large

None of those are relevant.

> How can i make sure the forces dont get that large? I dont know what these 3 
> causes are.
>  I have not recognized where the problem is and fixed it yet. It is wasting 
>my time a lot. My protein and ligand were intact . so what is its 
>problem?would you please help me? and introduce me an appropriate reference to 
>be expert in GROMACS?

Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?

-Justin

-- 
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }Hi justin
 Thank you for replyActually, since i am a new gromacs user, i used all .mdp 
files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial 
in gromacs. And did all the steps and issued all commands that said in this 
tuturial . I also generated my ligand topology by PRODRG and edited the charges 
and charge groups . To edit atome charge, according to aminoacids.rtp file, i 
considered what my atomes are bonded to , in order to best give their charge. 
Then , regarding to the article : Practical considerations for building 
GROMOS-compatible small-molecule topologiesEditted the charge groups , but i 
think , maybe i was wrong in specifying charg groups. In addition, i noticed 
that there was a wrong bond in the gromacs topology ang gromacs cordinate 
files, so i corrected them but i dont know if i did right?  These are all that 
i did. I dont know more about generating ligand topology but informatin that 
said in this tuturial. If you let me, send my ligand topology file to you? 
With best regardsFarial

Sent from Yahoo Mail for iPhone


On Friday, July 14, 2017, 2:59 PM, Justin Lemkul  wrote:



On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi Justin
> Thank you so much for your reply about minimize ligand in vacuoaccording to 
> :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
>( one or more water molecules can not to be settled . check for bad contacts 
>or reduce time step))I checked my protein in desired solvent as i noticed in 
>the previous mail, and it was stable. i minimized my ligand too in vacuo with 
>the .mdp file which you advised me, it was minimized well and monitored by 
>pymol, its configuration was ok.
> In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
> error in 2 steps.then, reduced the temperature to 100 k , but the same error 
> displayed again.
> Actually, I cant understand some advices and causes in this site. like:
> I dont understand  some of causes and advices in this site, include:1) you 
> are doing particle insertion in free energy calculations without using soft 
> core2) your position restraints are to coordinates too different from those 
> present in the system3) Make sure the forces don't get that large

None of those are relevant.

> How can i make sure the forces dont get that large? I dont know what these 3 
> causes are.
>  I have not recognized where the problem is and fixed it yet. It is wasting 
>my time a lot. My protein and ligand were intact . so what is its 
>problem?would you please help me? and introduce me an appropriate reference to 
>be expert in GROMACS?

Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?

-Justin

-- 
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Ramping down the restraint on molecules

[Lakshman Ji Verma]

Thanks Justin

Regards,
Lakshman

On Thu, Jul 13, 2017 at 8:27 PM, Justin Lemkul  wrote:

>
>
> On 7/13/17 10:37 AM, Lakshman Ji Verma wrote:
>
>> Dear all,
>>
>> I want to ramp down the restraint on the two molecules from 1000k to 0 on
>> some time interval so that restraint is removed gradually. My colleagues
>> said that it can be done with single md parameter file in LAMMPS and NAMD.
>> Can this be done using a single .mdp file in Gromacs too?  Or I will have
>>
>
> No.
>
> to prepare different .mdp and restraint file for each step.
>>
>
> Yes.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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[gmx-users] 'fudgeQQ' parameter in the topology file

[Sara Del Galdo]

Dear Gromacs user,

I read from the Gromacs Manual (version 5.1.2) that, while fudgeLJ is used
only when
generate pairs is set to ‘yes’, fudgeQQ is always used.

1. If I set  fudgeQQ = 0.0, will gromacs annulate the 1-4 interactions ?

2. If I explicitly insert a (Coulomb 1-4) scaling factor in my [pairs]
section in the topology file, will Gromacs use both the scaling factor and
fudgeQQ ?
For example, how Gromacs will manage the following case (where the 4-th
coloumn in my pairs section is the scaling factor mentioned above)?

 [ defaults ]
; nbfunc   comb-rule   gen-pairs  fudgeLJ  fudgeQQ
 1   2  no   0.5 0.8333
[ pairs ]
; 1-4 interactions
  1   8   20.833   -0.5360.1150.2875 0.14940
  1   9   20.833   -0.5360.1170.2875 0.14940
  1  10   20.833   -0.536   -0.0330.3400 0.22821
  1  23   20.833   -0.536   -0.3270.3105 0.39527
  :  :   :::::  :


Thanks in advance.

Sara
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Re: [gmx-users] Concrete pull code explanation needed

[Justin Lemkul]

On 7/13/17 8:11 PM, Du, Yu wrote:





-Original Messages-
From: "Justin Lemkul" 
Sent Time: Thursday, July 13, 2017
To: gmx-us...@gromacs.org
Cc:
Subject: Re: [gmx-users] Concrete pull code explanation needed



On 7/11/17 8:23 PM, Du, Yu wrote:

On 7/10/17 11:19 PM, Du, Yu wrote:

Dear Justin and gmx users,


I have gone through mdp-option and Justin A. Lemkul's COM pulling tutorial 
serveral times.


The following is Justin's pull code.


; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups= 1 2
pull_coord1_dim = N N Y
pull_coord1_rate= 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start   = yes   ; define initial COM distance > 0


My understanding lists as follows,


Justin defines two pull groups, with `pull-ngroups = 2`, each of them has a 
name in the index.ndx generated by `gmx make_ndx -f npt.gro`and their names are 
defined by `pull_group1_name = Chain_B` and `pull_group2_name = Chain_A`.


My question is about the definition of pulling coordination and the orientation 
of pulling force.


1) I learnt from [gmx-users] Change to umbrella sampling pull code，
"You need: pull-coord1-groups = 1 2 otherwise the reaction coordinate is undefined, 
or otherwise defaults to the entire system, I can't remember which. -Justin"


I know it's a plot :) in the input.pdb that proteins are placed exquisitely 
along the z-axis which is the same as the pulling coordinate but it makes pull 
code confused and here I need a concrete explanation.
1.The pull coordinate is the line that connects COM of group1 and group2 with 
`pull_coord1_groups= 1 2`.
OR 2. The pull coordinate is the z axis with `pull_coord1_dim = N N Y`.
Which is correct?



The z-component of the vector connecting the COMs of the two groups.



2)Then turn to the orientation of pulling forces.
My understanding is that force1 acts on pull_group1, force2 acts on pull_group2 
and the orientation of force 1 and 2 is opposite, both forces have a rate of 
10nm per ns.
Is my understanding and the below schematic draw right?



There is one force.  It acts on the spring connecting the two groups.



How does the spring connect the two groups? Does the spring link to the COM of 
the whole two groups?


Yes.


How does Gromacs define the orientation of the force of pulling? Or by default 
is the pulling force just positive along the z axis with `pull_coord1_geometry 
= distance` and `pull_coord1_dim = N N Y`?



This is not the default, but it is precisely what is specified by those .mdp
settings.




Could you please show which line specifies the orientation of the pulling 
force? Is it the positive `pull_coord1_rate`? So `pull_coord1_rate` can be 
either positive or negative?



pull_coord1_dim or pull_coord1_vec, depending on the geometry used.

Pull rates can be positive (to increase distance between the groups over time), 
negative (to decrease the distance), or zero (to maintain a distance).  The rate 
has nothing to do with the direction.






Z-axis-0-5--->---positive-orientation--->-25-->
  


The last question is about the umbrella sampling.
I learnt from [gmx-users] Re: doubt about your Umbrella Sampling tutorial that 
it's ok to remove the pores of Chain B during the US. But in longer simulation 
time and in the periodical box, will the COM of Chain B and A be affacted by 
the boundary? and then affact the calculation of US potential?



The tutorial system won't work if you turn off the restraint.  Eventually the
system will rotate and the groups will cross periodic boundaries, which will
cause the chosen pull geometry to fail.  So the restraints serve a dual purpose:
(1) to mimic the stability of larger amyloid assemblies and (2) to reduce the
system size, as several hundred thousand atoms was not feasible for me at the 
time.



So your point is that during US, we can't remove the Chain B's restrain. Right?


*For this specific case* yes.


During US, is there any means to study the flexiblity of both groups? (i.e. 
there is no restrain on both groups except the umbrella potential between them 
and at the same time both groups will not cross periodic boundaries and will 
not affact the umbrella potential geometry, which is a necessary part of my 
study)


Normally one should not apply any position restraints, except in niche cases
like mine.



During US, Why did you use Chain B's position restrain? Why is your case 
specific?



Please read the paper I linked from the tutorial and the many, many times I've 
explained this on the mailing list.

Re: [gmx-users] Non-periodic COM Pulling

[Justin Lemkul]

On 7/13/17 1:56 PM, Daniel Kozuch wrote:

Justin,

It was my understanding that direction-periodic would not allow for the NPT
ensemble (which I would like to use if possible, and why I did not use it
in the first place). Is there a way around this?



Not that I'm aware of.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Equilibration

[Justin Lemkul]

On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:

Hi Justin
Thank you so much for your reply about minimize ligand in vacuoaccording to 
:http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
( one or more water molecules can not to be settled . check for bad contacts or 
reduce time step))I checked my protein in desired solvent as i noticed in the 
previous mail, and it was stable. i minimized my ligand too in vacuo with the 
.mdp file which you advised me, it was minimized well and monitored by pymol, 
its configuration was ok.
In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
error in 2 steps.then, reduced the temperature to 100 k , but the same error 
displayed again.
Actually, I cant understand some advices and causes in this site. like:
I dont understand  some of causes and advices in this site, include:1) you are 
doing particle insertion in free energy calculations without using soft core2) 
your position restraints are to coordinates too different from those present in 
the system3) Make sure the forces don't get that large


None of those are relevant.


How can i make sure the forces dont get that large? I dont know what these 3 
causes are.
  I have not recognized where the problem is and fixed it yet. It is wasting my 
time a lot. My protein and ligand were intact . so what is its problem?would 
you please help me? and introduce me an appropriate reference to be expert in 
GROMACS?


Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] frozen ligand for free energy calculations

[Justin Lemkul]

On 7/13/17 11:51 AM, Ahmet Yildirim wrote:

OK, thanks. Which of the following option do you suggest me under
intermolecular interactions?
1) function type 6, 1 and 1 for [ bonds ], [ angles ] and [ dihedrals ]
respectively
2) function type 6, 1 and 1 for [ bonds ], [ angle_restraints ] and[
dihedral_restraints ] respectively
3) function type 10, 1 and 1 for [ distance_restraints ], [
angle_restraints ] and [ dihedral_restraints ] respectively



Bonds, angles, and dihedral restraints should work fine.

-Justin




On 13 July 2017 at 17:21, Justin Lemkul  wrote:




On 7/13/17 9:59 AM, Ahmet Yildirim wrote:


Dear users,

I come across with an issue when I try to do free energy calculations. The
issue is about the roto-translational motions of the ligand in the
decoupled state. I mean the ligand doesn't stay stable in the binding
pocket as in the coupled state.
It seems that the restraints that are applied on the atoms of the protein
and ligand under [ intermolecular_interactions ] part (an example of it is
below) in the compex top file aren't sufficient to keep the ligand from
repositioning/rotation with respect to the protein in the decoupled state.
Even one, two and three sets of restraints couldn't solve the issue.

[ intermolecular_interactions ]
[ bonds ]
; ai  ajtype   bA   kA   bBkB
629 3 6  0.5970.0  0.597 4184.0

[ angles ]
; ai  ajaktype   thA  fcA  thBfcB
281   629 3 1   37.50.0   37.5  41.84
629 321 1  121.50.0  121.5  41.84

[ dihedrals ]
; ai aj akaltypethA fcA   thB   fcB
249   281   629 3 2 -147.40.0 -147.4  41.84
281   629 321 2  -60.50.0  -60.5  41.84
629 32116 2 -153.90.0 -153.9  41.84



Here, with function type 2, you're specifying improper dihedrals.  This
isn't going to be what you want.  You probably want to be using a series of
dihedral restraints, not actual dihedrals.



I would try to freeze the ligand in the decoupled state in the canonical

ensemle with the above restrains under [ intermolecular_interactions ] but
I am not sure whether that makes sense or not? Justin says (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
/2013-August/083647.html):

"...Anything that is frozen, by definition, never has its position
updated.  Under the influence of
pressure coupling, other particles around the frozen group can have their
positions scaled and thus collide with the frozen group, which has
remained
in
its original location". I think I can use the frozen ligand in both
coupled
and decoupled state? And I should take into consideration the effect of
the
frozen ligand on the free energy calculation, right?



By doing this, you're negating any conformational sampling of the ligand,
therefore its entropy is wrong, and if the protein drifts and the ligand
stays put (because it's frozen) that's a fairly useless state.  The
appropriate strategy is a system of intermolecular interactions, but they
need to be properly defined.  As well, the choice of atoms can be
significant, e.g. dx.doi.org/10.1021/ci300505n and references therein.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] LINCS warning during constrained md

[edesantis]

Dear Mark,
I understand your point,
but I've used the Martini-backmapping protocol written in the initram.sh 
wrapper found in Martini documentation 
(https://github.com/Tsjerk/MartiniTools/blob/master/initram.sh), so it 
seems to me quite weird that it was not working in the proper manner.



an other problem is that I've to convert some thousands of structure 
extracted from the martini trajectory,
I thought that this kind of conversion doesn't require to much effort, 
so for this reason I thought that the posres flag was useful to limit 
the computational time... maybe I'm wrong


Can I avoid to use constrained bonds and use only posres? what do you 
think about?




in addition, for you, how many steps of md have I to perform to do this 
kind of equilibration? have I to look necessarily at the rmsd in each 
trajectory? I'd like to have a robust protocol to do all the conversions 
in an automatic way...


thank you again for your suggestions
regards,
Emiliano



On 2017-07-12 17:23, Mark Abraham wrote:

Hi,

I would avoid using the combination of position restraints and 
constrained
bonds with an input structure that is not necessarily consistent with 
the

constraints. That's a recipe for large forces. I wouldn't use position
restraints in such a process unless I had some reason to believe that 
my
starting structure was special *and* saw a large deformation if I 
didn't
use the restraints. If I saw the deformation, I would wonder why I 
thought

it was special.

If you're trying to relax a thing, let it relax. :-) If something 
strange
happens, consider that when it has happened. Obviously that means you 
want
to look at what happens when you did your equilibration, but you were 
going

to do that anyway. Right? ;-)

Mark

On Wed, Jul 12, 2017 at 5:17 PM edesantis  
wrote:



hi,

I've seen with vmd the gro file generated after the transformation, 
and

after the 2 steps of minimization,
it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there 
are

some atoms far away from the rest of the protein, while this is not
happening if I comment the restrains part


do you understand why??

thank you again,
Emiliano



On 2017-07-12 16:29, Mark Abraham wrote:
> Hi,
>
> Those are all good things, but have you actually got out a molecular
> viewer
> and looked at the input and output of your resolution conversion?
>
> Mark
>
> On Wed, Jul 12, 2017 at 4:25 PM edesantis 
> wrote:
>
>> Hi,
>> thanks for the prompt answer,
>>
>>
>> I've found the same problem even if I try to convert the coarse
>> grained
>> pdb obtained from martinize.py, so in that case it should be not a
>> problem to have the conversion, for this reason I though it is a
>> methodological problem...
>>
>> I've seen the blowing-up issues , but I think:
>> - the timestep is enough small  (0.0002)
>> -the system should be enough minimized via the previous steps (in fact
>> the sd converged to the machine precision in both cases, actually the
>> potential energy is ~10^5, but I don't know how to reduce it, I tried
>> a
>> cg after the sd, but the proble is still there)
>> -there in not any pressure coupling
>> -I've tried a different temperature coupling (berensden, nose-hoover)
>> and it doesn't work
>> - the md stops at the first step, so there is not any .edr file
>> produced
>> to be looked at
>>
>>
>>
>> I don't know what else to do...
>>
>> maybe, do you know another conversion protocol to use??
>>
>>
>> thank you again
>> Emiliano
>>
>> On 2017-07-12 15:11, Mark Abraham wrote:
>> > Hi,
>> >
>> > Sounds like you might be
>> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because
the
>> > conversion doesn't work for your configuration. You should start by
>> > doing a
>> > visual check of the configuration for sanity, then follow the advice
in
>> > that link.
>> >
>> > Mark
>> >
>> > On Wed, Jul 12, 2017 at 3:04 PM edesantis 
>> > wrote:
>> >
>> >> dear all,
>> >>
>> >> I am facing a problem with the conversion from Martini CG
>> >> representation
>> >> to All-atomistic one.
>> >>
>> >> I am using the initram.sh wrapper around the backward.py.
>> >>
>> >> There is a LINCS warning problem when the energy relaxation is
>> >> performed
>> >> using position restrained md
>> >> (I've also tried to run grompp and mdrun commands directly from the
>> >> terminal and the error persists, so it is not a wrapper problem).
>> >>
>> >> this is the .mdp file generated by the script:
>> >>
>> >> "define   = -DPOSRES
>> >> integrator   = md
>> >> nsteps   = 500
>> >> dt   = 0.0002
>> >> pbc  = xyz
>> >>
>> >> rcoulomb = 0.9
>> >> rlist= 0.9
>> >> rvdw = 0.9
>> >>
>> >> tcoupl   = v-rescale
>> >> ref_t= 200
>> >> tau_t= 0.1
>> >> 

Re: [gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

The graphene is 9*9 nm, and I proposed the box to be 11*11 nm. Do you mean that 
the box dimensions are small and thats the problem?
Thanks,Mohammad
  From: Alex 
 To: Discussion list for GROMACS users ; Discussion list 
for GROMACS users  
 Sent: Friday, 14 July 2017, 11:31:06
 Subject: Re: [gmx-users] NPT problem
   

>
> I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT 
> -noparam -pbc" for generating the topology. then I used "gmx editconf 
> -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating 
> the box
>
And where did "-box 11 11 11" come from? For pbc to work the box in your 
case has to be a certain size corresponding to the graphene dimensions. 
And no, it is not simply its approximate X-Y dimensions.

Alex

>
> 
> *From:* Alex 
> *To:* Discussion list for GROMACS users ; 
> Mohammad Roostaie 
> *Sent:* Thursday, 13 July 2017, 22:51:48
> *Subject:* Re: [gmx-users] NPT problem
>
> Also, that tutorial's parameters that are completely wrong for 
> graphene. For bulk graphene bond types I suggest:
>
> CJ    CJ      1    0.14200  420420.0
>
> For bulk angles:
>
> CJ    CJ    CJ      1  120.000    659.346
>
> For bulk dihedrals:
>
>  CJ    CJ    CJ    CJ      3 17.30770  0.0 -17.30770  
> 0.0 0.0  0.0
>
> These are parameters obtained from a Taylor-expanded optimized 
> Tersoff-Brenner potential. Please count the number of bonds and 
> dihedrals in your graphene model, as produced by x2top. If the number 
> of dihedrals divided by the number of bonds gives you a number, say, 
> equal to m, then multiply the dihedral parameters by that number. And 
> do NOT use bond constraints -- you are simulating a crystal.
>
> Alex
>
> On Thu, Jul 13, 2017 at 10:45 AM,  > wrote:
>
>    Hi All GROMACS users,
>
>
>
>    I created graphene with nanotube modeler then I created a force
>    field for graphene based on OPLS (by using this link and its
>    parameters: http://chembytes.wikidot.com/ grocnt
>    ). I generated the topology
>    file using x2top command. I put the graphene inside a box of water
>    (TIP3P) which was larger than the graphene dimension with 1000
>      (kJ/mol nm^2) position restraint on all the atoms, and I
>    performed the energy minimization and NVT equilibrations (in order
>    to get an optimized structure of the graphene for further
>    simulations). The results of both of them were good (energy level
>    has reached a negative value with the order of 6 and the
>    temperature has converged the preferred value). But, when I run
>    the NPT equilibration, the results are not good (the pressure and
>    density fluctuated very much and the averaged values are so far
>    from the preferred ones). Also, during the NPT run, I received
>    these messages:
>
>
>    step 53965: Water molecule starting at atom 127424 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 141454: Water molecule starting at atom 53366 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 141483: Water molecule starting at atom 53366 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 323815: Water molecule starting at atom 30509 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 323816: Water molecule starting at atom 30509 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 323818: Water molecule starting at atom 30509 can not be settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 355712: Water molecule starting at atom 121748 can not be
>    settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 355714: Water molecule starting at atom 121748 can not be
>    settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote pdb files with previous and current coordinates
>
>
>
>    step 355716: Water molecule starting at atom 121748 can not be
>    settled.
>
>    Check for bad contacts and/or reduce the timestep if appropriate.
>
>    Wrote 

Re: [gmx-users] NPT problem

[Alex]

I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT 
-noparam -pbc" for generating the topology. then I used "gmx editconf 
-f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating 
the box


And where did "-box 11 11 11" come from? For pbc to work the box in your 
case has to be a certain size corresponding to the graphene dimensions. 
And no, it is not simply its approximate X-Y dimensions.


Alex




*From:* Alex 
*To:* Discussion list for GROMACS users ; 
Mohammad Roostaie 

*Sent:* Thursday, 13 July 2017, 22:51:48
*Subject:* Re: [gmx-users] NPT problem

Also, that tutorial's parameters that are completely wrong for 
graphene. For bulk graphene bond types I suggest:


CJCJ  10.14200   420420.0

For bulk angles:

CJ CJ CJ  1   120.000659.346

For bulk dihedrals:

  CJ CJ CJ CJ  3 17.30770   0.0 -17.30770   
0.0 0.0   0.0


These are parameters obtained from a Taylor-expanded optimized 
Tersoff-Brenner potential. Please count the number of bonds and 
dihedrals in your graphene model, as produced by x2top. If the number 
of dihedrals divided by the number of bonds gives you a number, say, 
equal to m, then multiply the dihedral parameters by that number. And 
do NOT use bond constraints -- you are simulating a crystal.


Alex

On Thu, Jul 13, 2017 at 10:45 AM, > wrote:


Hi All GROMACS users,



I created graphene with nanotube modeler then I created a force
field for graphene based on OPLS (by using this link and its
parameters: http://chembytes.wikidot.com/ grocnt
). I generated the topology
file using x2top command. I put the graphene inside a box of water
(TIP3P) which was larger than the graphene dimension with 1000
 (kJ/mol nm^2) position restraint on all the atoms, and I
performed the energy minimization and NVT equilibrations (in order
to get an optimized structure of the graphene for further
simulations). The results of both of them were good (energy level
has reached a negative value with the order of 6 and the
temperature has converged the preferred value). But, when I run
the NPT equilibration, the results are not good (the pressure and
density fluctuated very much and the averaged values are so far
from the preferred ones). Also, during the NPT run, I received
these messages:


step 53965: Water molecule starting at atom 127424 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 141454: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 141483: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 323815: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 323816: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 323818: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 355712: Water molecule starting at atom 121748 can not be
settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 355714: Water molecule starting at atom 121748 can not be
settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 355716: Water molecule starting at atom 121748 can not be
settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 355718: Water molecule starting at atom 121748 can not be
settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 469414: Water molecule starting at atom 101579 can not be
settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 469416: Water molecule starting at atom 101579 

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

[Alex]

Hi Jason,

I didn't have time to look at all of those papers, but look for instance 
at eq. (2) in Hilder et al's paper and the definition of the f_dmp 
function on the right -- this tapers off short-range interactions for 
close neighbors. I am not sure if this particular function results in 
any serious difference (I think, given the value of R_r, it was designed 
pretty much exactly to remove all nonbonded interactions closer than 
second neighbor), but the point is that Gromacs doesn't use anything 
like this. As a result, many things cannot be translated into Gromacs 
FFs "as is," requiring a fairly broad range of effort from mild 
tinkering all the way to complete reparameterization.. Even then the 
best one can hope for with Gromacs when applied to the actual properties 
of crystals is structure stability and correct bond lengths -- nothing 
beyond that. This is really more of a general comment, because more and 
more people are trying to simulate solid-state structures with Gromacs.


Best of luck!

Alex


On 7/13/2017 6:43 PM, Jason Zhu wrote:

Dear Alex,

Many thanks for your replies and helping.

I totally agree with your comments about infinite molecules and 
periodic boundary condition.


Here in our simulations, the hBN sheet covers the box dimensions 
(6nm*6nm) without free edges. By using PBC and "periodic-molecules = 
yes", we could calculate the surface energy of hBN sheet without 
effects of edges.


The parameters of force field we are using are borrowed from the 
following papers. We introduced them into the Gromos force field. We 
are having a new publication using this modified force field in which 
all the parameters are shown explicitly. I could send it to you when 
it is published online. The functions and parameters are fitted by the 
setting of "nrexcl=3" in these papers. We couldn't make any changes 
for this. But we could try to use larger value of "nrexcl" to fit the 
force field of hBN and include short-range non-bonded interactions 
into bonded interactions. Thank you for your suggestions.


1. Hilder, T. A. et al. Validity of current force fields for 
simulations on boron nitride nanotubes. IET Micro & Nano Letters 5, 
150-156, doi:10.1049/mnl.2009.0112 (2010).


2. Kamath, G. & Baker, G. A. Are ionic liquids suitable media for 
boron nitride exfoliation and dispersion? Insight via molecular 
dynamics. RSC Advances 3, 8197-8202, doi:10.1039/c3ra40488a (2013).


3. Wu, J., Wang, B., Wei, Y., Yang, R. & Dresselhaus, M. Mechanics and 
Mechanically Tunable Band Gap in Single-Layer Hexagonal Boron-Nitride. 
Materials Research Letters 1, 200-206, 
doi:10.1080/21663831.2013.824516 (2013).


Best,
Jason


Message: 5
Date: Wed, 12 Jul 2017 19:12:26 -0600
From: Alex >
To: Discussion list for GROMACS users >

Subject: Re: [gmx-users] Periodic Molecule's Free Energy Calculation
Error
Message-ID: <4b927ef2-9a56-6655-8053-d284cf88b...@gmail.com 
>

Content-Type: text/plain; charset=utf-8; format=flowed


>
> I wonder if the "couple-intramol = yes" is a must. Does it have any
> influence on the output results if we turn off the intra-molecular
> non-bonded interactions of a large infinite molecule?
>
The answer to your question has nothing to do with Gromacs, but with
understanding the difference between crystals and biomolecules (for
which Gromacs was designed).
Also (unrelated), it is a common misconception to believe that PBC makes
something infinite -- the effective size of your system is entirely
determined by the supercell size (proof: consider the ripples in hBN and
determine the lowest wavelength of the ripple that can propagate -- it
is commensurate with the box size). In an infinite system, you can have
an immensely long wave (though not infinite, as shown by Landau a while
back). PBC does not make anything infinite, it is a mathematical way of
avoiding surfaces.
>
> There is no universal force field for HBN, so I am using a modified
> gromos54a7_atb force field, i.e., manually adding the parameters for
> boron and nitrogen to the bonded & nonbonded .itp files.
Oh, I know that there is no force fields for these structures. ;) My
question was about which Gromacs ff you were using to insert your
parameters, and, most importantly, where those parameters came from.

> The parameters are obtained from literature.
>
What literature? All bio-style ff adaptations of solid-state potentials
(e.g. Tersoff-Brenner for hBN) I am aware of make it very clear that
"intramolecular" interactions between atoms sharing up to a fairly
distant covalently bound neighbor are limited to bonds and angles. This
comes from the math involved in developing potentials for crystals.
There was a recent question regarding this very problem here, which was
solved by setting a larger nrexcl value. In your case, you solved it
with turning off 

Re: [gmx-users] NPT problem

[‪Mohammad Roostaie‬ ‪]

Hi Alex, Thank you for your reply.
By the term "results were good or not" I meant that whether the temperature, 
pressure, and density have converged to the preferred values or not (I 
mentioned it in the parenthesis, too).
I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT -noparam 
-pbc" for generating the topology. then I used "gmx editconf -f grvmdn.pdb -o 
gr.gro -box 11 11 11 -angles 90 90 90" for creating the box then I filled it 
with water with "gmx solvate -cp gr.gro -cs spc216.gro -o gr_solv.gro -p 
topol.top" command. The x2top does not require the box dimensions. Should I use 
the "-pbc" option in editconf, too? Do you mean that first I should perform EM, 
NVT, NPT, and MD run on the graphene alone without water and any position 
restraints? Also, I followed the tutorial step by step. Also, I used it since 
this tutorial is mentioned on Gromacs website. Actually, I think that in this 
tutorial, the purpose is to generate a force filed for graphene based on OPLS 
force field. Moreover, I added the ffbonded.itp, ffnonbonded.itp, and tip3p.itp 
files from OPLS-AA force field to the directory for the water molecules. Also, 
after optimization of the graphene, I want to put a peptide inside the box, so 
I should add those files, also I think that I should add the aminoacids.rtp for 
the peptide in order to use a unique force field for all the molecules and not 
to use different force fields.
Kind regards,Mohammad



  From: Alex 
 To: Discussion list for GROMACS users ; Mohammad 
Roostaie  
 Sent: Thursday, 13 July 2017, 22:51:48
 Subject: Re: [gmx-users] NPT problem
   
Also, that tutorial's parameters that are completely wrong for graphene. For 
bulk graphene bond types I suggest:
  CJ    CJ      1    0.14200   420420.0 

For bulk angles:
  CJ     CJ     CJ      1   120.000    659.346  

For bulk dihedrals:
  CJ     CJ     CJ     CJ      3     17.30770   0.0 -17.30770   0.0   
0.0   0.0
These are parameters obtained from a Taylor-expanded optimized Tersoff-Brenner 
potential. Please count the number of bonds and dihedrals in your graphene 
model, as produced by x2top. If the number of dihedrals divided by the number 
of bonds gives you a number, say, equal to m, then multiply the dihedral 
parameters by that number. And do NOT use bond constraints -- you are 
simulating a crystal.
Alex
On Thu, Jul 13, 2017 at 10:45 AM,  wrote:

Hi All GROMACS users,


 
I created graphene with nanotube modeler then I created a force field for 
graphene based on OPLS (by using this link and its parameters: 
http://chembytes.wikidot.com/ grocnt). I generated the topology file using 
x2top command. I put the graphene inside a box of water (TIP3P) which was 
larger than the graphene dimension with 1000  (kJ/mol nm^2) position restraint 
on all the atoms, and I performed the energy minimization and NVT 
equilibrations (in order to get an optimized structure of the graphene for 
further simulations). The results of both of them were good (energy level has 
reached a negative value with the order of 6 and the temperature has converged 
the preferred value). But, when I run the NPT equilibration, the results are 
not good (the pressure and density fluctuated very much and the averaged values 
are so far from the preferred ones). Also, during the NPT run, I received these 
messages:


step 53965: Water molecule starting at atom 127424 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141454: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 141483: Water molecule starting at atom 53366 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323815: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323816: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 323818: Water molecule starting at atom 30509 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355712: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates


 
step 355714: Water molecule starting at atom 121748 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files 

Re: [gmx-users] xtc trajectory only

[Mark Abraham]

Hi,

What does gmx check or dump tell you about what is in the files you're
writing?

Mark

On Fri, 14 Jul 2017 08:30 Atila Petrosian  wrote:

> Dear Mark,
> Thanks for your answer.
>
> I deleted (nstxout = 5000) in mdp file. But still both of xtc and
> trr trajectory files were created.
>
> Best,
> Atila
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] xtc trajectory only

[Atila Petrosian]

Dear Mark,
Thanks for your answer.

I deleted (nstxout = 5000) in mdp file. But still both of xtc and
trr trajectory files were created.

Best,
Atila
-- 
Gromacs Users mailing list

* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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