[gmx-users] How does gromacs checkpoint works

[Husen R]

Hi all,

For academic purpose, I'm wondering how does checkpoint feature in Gromacs
works ?
is there any resource/tutorial that I can learn ?


Thank you in advance,


Husen
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[gmx-users] restart error

[ingram]

Dear Grommunity,

When I try and restart with the command "mpiexec -np 192 mdrun_mpi -v 
-deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir 
simann59 simann60 simann61 simann62 simann63 simann64 simann65 simann66 
simann67 simann68 simann69 simann70 simann71 simann72 simann73 simann74" 
I get the error " Fatal error: Can't read 187477 bytes of 
'md_golp_vacuo.log' to compute checksum". I then see that the 
simulations where this occurs are much behind the others, for example:


   Step   Time Lambda
   310031000.00.0
   Step   Time Lambda
   320032000.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0
   Step   Time Lambda
   575057500.00.0

I have already posted about this issue, and I thought I had made the 
mistake. But I believe this to be a bug in GROMACS but please tell me if 
this still seems like a user error and not GROMACS. I am using GROMACS 
5.1.2


Best

Teresa

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Re: [gmx-users] least-squares fitting the second structure on the reference structure

[Qasim Pars]

Hi Tsjerk,

Thanks, I know that. I was wondering how does a second structure (for
instance third frame) fit mathematically onto the reference structure? I
understand the least-square fitting for only one data set but I couldn't
understand the the least-square fitting for two data sets that fit on each
other's.

Cheers,

On 23 June 2016 at 00:14, Tsjerk Wassenaar  wrote:

> Hi Qasim,
>
> If you fit a trajectory, with trjconv -fit rot+trans, then each frame is
> fit onto the reference.
>
> Hope it helps,
>
> Tsjerk
>
> On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars  wrote:
>
> > Dear users,
> >
> > From GROMACS online manual:
> > gmx confrms computes the root mean square deviation (RMSD) of two
> > structures after least-squares fitting the second structure on the first
> > one.
> >
> > My question is how GROMACS does least-squares fitting the second
> structure
> > (each frame of trajectory) on the first one (reference structure)? It
> > calculates the least-squares fitting of the second structure and the
> first
> > one seperately?
> >
> > Thanks for your helps.
> > --
> > Gromacs Users mailing list
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> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Radial Distribution Function - is there symmetry?

[Dan Gil]

Thanks for the great explanation!

On Wed, Jun 22, 2016 at 5:14 PM, Mark Abraham 
wrote:

> Hi,
>
> In general it won't be. Take a  pure NaCL cubic crystal - G(r)_NaCl is the
> same as G(r)_ClNa by symmetry. Now take an identical crystal with any
> single Cl replaced by Br (or half of them, or whatever) and assume all the
> lattice dimensions remain the same. G(r)_ClNa is the same as before, but
> G_(r)_NaCl cannot be the same as before. Or try it on your favourite
> simulation trajectory :-)
>
> Mark
>
> On Wed, Jun 22, 2016 at 11:06 PM Dan Gil  wrote:
>
> > Hi,
> >
> > I am calculating the radial distribution function, and I am wondering if
> > G(r)_jk = G(r)_kj. I always assumed that it was, and when I looked at the
> > equation it seemed to be the case. But I am having trouble finding
> sources
> > that state G(r)_jk = G(r)_kj, therefore I wanted to ask for your opinion.
> >
> > Best Regards,
> >
> > Dan
> > --
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Re: [gmx-users] least-squares fitting the second structure on the reference structure

[Tsjerk Wassenaar]

Hi Qasim,

If you fit a trajectory, with trjconv -fit rot+trans, then each frame is
fit onto the reference.

Hope it helps,

Tsjerk

On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars  wrote:

> Dear users,
>
> From GROMACS online manual:
> gmx confrms computes the root mean square deviation (RMSD) of two
> structures after least-squares fitting the second structure on the first
> one.
>
> My question is how GROMACS does least-squares fitting the second structure
> (each frame of trajectory) on the first one (reference structure)? It
> calculates the least-squares fitting of the second structure and the first
> one seperately?
>
> Thanks for your helps.
> --
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>



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Re: [gmx-users] Radial Distribution Function - is there symmetry?

[Mark Abraham]

Hi,

In general it won't be. Take a  pure NaCL cubic crystal - G(r)_NaCl is the
same as G(r)_ClNa by symmetry. Now take an identical crystal with any
single Cl replaced by Br (or half of them, or whatever) and assume all the
lattice dimensions remain the same. G(r)_ClNa is the same as before, but
G_(r)_NaCl cannot be the same as before. Or try it on your favourite
simulation trajectory :-)

Mark

On Wed, Jun 22, 2016 at 11:06 PM Dan Gil  wrote:

> Hi,
>
> I am calculating the radial distribution function, and I am wondering if
> G(r)_jk = G(r)_kj. I always assumed that it was, and when I looked at the
> equation it seemed to be the case. But I am having trouble finding sources
> that state G(r)_jk = G(r)_kj, therefore I wanted to ask for your opinion.
>
> Best Regards,
>
> Dan
> --
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[gmx-users] Radial Distribution Function - is there symmetry?

[Dan Gil]

Hi,

I am calculating the radial distribution function, and I am wondering if
G(r)_jk = G(r)_kj. I always assumed that it was, and when I looked at the
equation it seemed to be the case. But I am having trouble finding sources
that state G(r)_jk = G(r)_kj, therefore I wanted to ask for your opinion.

Best Regards,

Dan
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Re: [gmx-users] selection of start or end terminus

[Justin Lemkul]

On 6/22/16 2:19 PM, Alexander Alexander wrote:

Thanks for your response.

And then why does "1" go wrong for a single amino acid in  zwitterions
form, as well? Isn't a single amino acid is a kind of peptide with only one
residue?



OPLS makes special changes to CA in the case of a zwitterion.  Look at the 
contents of the .tdb files and you will see where this comes from.


-Justin


Thanks.
Regards,
Alex

On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul  wrote:




On 6/22/16 12:53 PM, Alexander Alexander wrote:


Dear Gromacs user,

In the selection of start or end terminus type for peptide in OPLS_AA
force
field, what is the diffeece between option 0 and 1 in below list? I am
interested in the Zwitterion form, but the option 0 is Zwitterion form if
I
am not wrong!


Select start terminus type for 
 0: NH3+
 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
 2: NH2
 3: None

And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
system and then the whole system in not neutral anymore but 0 is fine. It
is clear below the differences and origination of the extra charge in
\alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
the topol file by replacing the opls_299 to opls_283 ... .?


Choosing 0.  :-)

; residue   1 LEU rtp LEU  q +1.0
  5  opls_293B  1LEU CA  10.25 12.011

 ;residue   7 GLU rtp GLU  q -2.0
 112   opls_283  7GLU CA 37   0.04 12.011


Choosing 1.   :-(

;residue   1 LEU rtp LEU  q +0.9
   5   opls_299  1LEU CA  1 0.15 12.011

;residue   7 GLU rtp GLU  q -1.9
112   opls_299  7GLU CA 37   0.15 12.011



pdb2gmx tells you what to do:

"only use with zwitterions containing exactly one residue"

Do you have more than one residue?  If yes, this is a wrong choice.

-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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--
==

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] selection of start or end terminus

[Alexander Alexander]

Thanks for your response.

And then why does "1" go wrong for a single amino acid in  zwitterions
form, as well? Isn't a single amino acid is a kind of peptide with only one
residue?

Thanks.
Regards,
Alex

On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul  wrote:

>
>
> On 6/22/16 12:53 PM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> In the selection of start or end terminus type for peptide in OPLS_AA
>> force
>> field, what is the diffeece between option 0 and 1 in below list? I am
>> interested in the Zwitterion form, but the option 0 is Zwitterion form if
>> I
>> am not wrong!
>>
>>
>> Select start terminus type for 
>>  0: NH3+
>>  1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
>> residue)
>>  2: NH2
>>  3: None
>>
>> And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
>> system and then the whole system in not neutral anymore but 0 is fine. It
>> is clear below the differences and origination of the extra charge in
>> \alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
>> the topol file by replacing the opls_299 to opls_283 ... .?
>>
>>
>> Choosing 0.  :-)
>>
>> ; residue   1 LEU rtp LEU  q +1.0
>>   5  opls_293B  1LEU CA  10.25 12.011
>>
>>  ;residue   7 GLU rtp GLU  q -2.0
>>  112   opls_283  7GLU CA 37   0.04 12.011
>>
>>
>> Choosing 1.   :-(
>>
>> ;residue   1 LEU rtp LEU  q +0.9
>>5   opls_299  1LEU CA  1 0.15 12.011
>>
>> ;residue   7 GLU rtp GLU  q -1.9
>> 112   opls_299  7GLU CA 37   0.15 12.011
>>
>>
> pdb2gmx tells you what to do:
>
> "only use with zwitterions containing exactly one residue"
>
> Do you have more than one residue?  If yes, this is a wrong choice.
>
> -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] selection of start or end terminus

[Justin Lemkul]

On 6/22/16 12:53 PM, Alexander Alexander wrote:

Dear Gromacs user,

In the selection of start or end terminus type for peptide in OPLS_AA force
field, what is the diffeece between option 0 and 1 in below list? I am
interested in the Zwitterion form, but the option 0 is Zwitterion form if I
am not wrong!


Select start terminus type for 
 0: NH3+
 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
 2: NH2
 3: None

And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
system and then the whole system in not neutral anymore but 0 is fine. It
is clear below the differences and origination of the extra charge in
\alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
the topol file by replacing the opls_299 to opls_283 ... .?


Choosing 0.  :-)

; residue   1 LEU rtp LEU  q +1.0
  5  opls_293B  1LEU CA  10.25 12.011

 ;residue   7 GLU rtp GLU  q -2.0
 112   opls_283  7GLU CA 37   0.04 12.011


Choosing 1.   :-(

;residue   1 LEU rtp LEU  q +0.9
   5   opls_299  1LEU CA  1 0.15 12.011

;residue   7 GLU rtp GLU  q -1.9
112   opls_299  7GLU CA 37   0.15 12.011



pdb2gmx tells you what to do:

"only use with zwitterions containing exactly one residue"

Do you have more than one residue?  If yes, this is a wrong choice.

-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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[gmx-users] selection of start or end terminus

[Alexander Alexander]

Dear Gromacs user,

In the selection of start or end terminus type for peptide in OPLS_AA force
field, what is the diffeece between option 0 and 1 in below list? I am
interested in the Zwitterion form, but the option 0 is Zwitterion form if I
am not wrong!


Select start terminus type for 
 0: NH3+
 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
residue)
 2: NH2
 3: None

And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
system and then the whole system in not neutral anymore but 0 is fine. It
is clear below the differences and origination of the extra charge in
\alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
the topol file by replacing the opls_299 to opls_283 ... .?


Choosing 0.  :-)

; residue   1 LEU rtp LEU  q +1.0
  5  opls_293B  1LEU CA  10.25 12.011

 ;residue   7 GLU rtp GLU  q -2.0
 112   opls_283  7GLU CA 37   0.04 12.011


Choosing 1.   :-(

;residue   1 LEU rtp LEU  q +0.9
   5   opls_299  1LEU CA  1 0.15 12.011

;residue   7 GLU rtp GLU  q -1.9
112   opls_299  7GLU CA 37   0.15 12.011

Many thanks.
Regards,
Alex
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Re: [gmx-users] Block averaging

[sun]

Allright Sir
Thank you

Sent from my iPhone

> On 22-Jun-2016, at 7:09 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 6/22/16 5:02 AM, sun wrote:
>> Hello users and experts I have completed a 200 ns protein ligand simulation
>> using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational
>> change in protein in the presence of ligand and the results are as expected
>> and correlates to previous references as well. So, shall i believe that
>> simulation is converged or there is need to do block averaging over time
>> intervals? If block averaging is required, the parameters like RMSD and
>> propensities for secondary structure are sufficient to conclude that
>> simulation is converged? Or could anyone please tell me a suitable procedure
>> for making blocks and how to average those. With Regards Suniba
> 
> Just because a simulation produces expected results does not mean it is 
> converged.  You must show that any quantities of interest from which you draw 
> your conclusions, are not systematically varying with time.
> 
> -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] Job Output stops being written during long simulations on HPC cluster

[Mark Abraham]

Hi,

Or the filesystem disappeared during the run...

Mark

On Wed, Jun 22, 2016 at 3:38 PM Szilárd Páll  wrote:

> I doubt it's a compiler issue, if anything it's more likely a
> system-component that's misbehaving (kernel, or file system). I'd try
> outputting to another fs, e.g. /tmp is there is one just to check.
> --
> Szilárd
>
>
> On Tue, Jun 21, 2016 at 1:35 AM, Benjamin Joseph Coscia
>  wrote:
> > Hi everyone,
> >
> > I have been attempting to run some long simulations on a supercomputer at
> > the University of Colorado at Boulder. I am trying to run simulations for
> > about 200 ns. I have done tests using 48 cores and 96 cores. In each case
> > output stops being written at the same time step (~50 million steps).
> This
> > is only about half of the simulation time I wanted. According to SLURM,
> the
> > job is still running days past when it stopped outputting.
> >
> > I checked how much space is being taken up by output files. The largest
> > file is the trajectory at ~0.2 GB. I am only outputting data every 1
> > million steps. I am convinced that this isn't a memory issue.
> >
> > I've reached out to the people who run the supercomputer and they are not
> > positive what is going on. One of the guys there ran a system trace on
> the
> > 'gmx_mpi mdrun' process and got the following output by looking at one of
> > the nodes that is hung up:
> >
> > [root@node0636 ~]# ps -ef | grep beco
> > root 2053 32739 0 20:48 pts/1 00:00:00 grep beco
> > beco4952 17561 17557 0 Jun14 ? 00:00:00 /bin/bash
> > /tmp/node0636/job1470980/slurm_script
> > beco4952 17597 17561 0 Jun14 ? 00:00:00 /bin/bash
> > /projects/beco4952/Gromacs/Pores/GitHub/Shell-Scripts/Build_and_Sim.sh -M
> > monomer1.pdb -I steep -S 5 -c verlet -t 10 -o 6 -r 3 -p 40 -P 4 -w 10
> > -l 20 -x 8.0 -y 8.0 -e 0.1 -T Equilibration in Vacuum -C verlet -i md -D
> > 0.002 -L 200 -f 100 -v v-rescale -K 300 -b berendsen -Y semiisotropic -B
> 1
> > -R 4.5e-5 -Z xyz -V 1 -n 8 -s off -m on
> > beco4952 18307 17597 0 Jun14 ? 00:00:00 /bin/sh
> > /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/mpirun -np 16
> gmx_mpi
> > mdrun -v -deffnm wiggle
> > beco4952 18313 18307 0 Jun14 ? 00:01:34 mpiexec.hydra -np 16 gmx_mpi
> mdrun
> > -v -deffnm wiggle
> > beco4952 18314 18313 0 Jun14 ? 00:00:00
> /curc/slurm/slurm/current/bin/srun
> > --nodelist
> > node0636,node0637,node0638,node0639,node0640,node0641,node0642,node0643
> -N
> > 8 -n 8 /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
> > --control-port node0636.rc.int.colorado.edu:41464 --pmi-connect
> lazy-cache
> > --pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
> > --enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
> > --proxy-id -1
> > beco4952 18315 18314 0 Jun14 ? 00:00:00
> /curc/slurm/slurm/current/bin/srun
> > --nodelist
> > node0636,node0637,node0638,node0639,node0640,node0641,node0642,node0643
> -N
> > 8 -n 8 /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
> > --control-port node0636.rc.int.colorado.edu:41464 --pmi-connect
> lazy-cache
> > --pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
> > --enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
> > --proxy-id -1
> > beco4952 18334 18329 0 Jun14 ? 00:01:00
> > /curc/tools/x86_64/rh6/software/impi/5.0.3.048/bin64/pmi_proxy
> > --control-port node0636.rc.int.colorado.edu:41464 --pmi-connect
> lazy-cache
> > --pmi-aggregate -s 0 --rmk slurm --launcher slurm --demux poll --pgid 0
> > --enable-stdin 1 --retries 10 --control-code 156865336 --usize -2
> > --proxy-id -1
> > beco4952 18354 18334 99 Jun14 ? 13-20:24:21 gmx_mpi mdrun -v -deffnm
> wiggle
> > beco4952 18355 18334 99 Jun14 ? 13-20:30:41 gmx_mpi mdrun -v -deffnm
> wiggle
> >
> > [root@node0636 ~]# strace -f -p 18354
> > Process 18354 attached with 9 threads - interrupt to quit
> > [pid 18380] futex(0x2b76d6461484, FUTEX_WAIT_PRIVATE, 1, NULL  > ...>
> > [pid 18378] futex(0x2b76d6462984, FUTEX_WAIT_PRIVATE, 1, NULL  > ...>
> > [pid 18375] futex(0x2b76d6475484, FUTEX_WAIT_PRIVATE, 3, NULL  > ...>
> > [pid 18374] futex(0x2b76d6476984, FUTEX_WAIT_PRIVATE, 3, NULL  > ...>
> > [pid 18368] restart_syscall(<... resuming interrupted call ...>
>  > ...>
> > [pid 18377] futex(0x2b76d6463e84, FUTEX_WAIT_PRIVATE, 3, NULL  > ...>
> > [pid 18364] restart_syscall(<... resuming interrupted call ...>
>  > ...>
> > [pid 18354] futex(0x2b76d6477784, FUTEX_WAIT_PRIVATE, 1, NULL  > ...>
> > [pid 18373] restart_syscall(<... resuming interrupted call ...>) = -1
> > ETIMEDOUT (Connection timed out)
> > [pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
> > [pid 18373] futex(0x2b76d0736a44,
> > FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 3631433, {1466303205,
> > 353534000}, ) = -1 ETIMEDOUT (Connection timed out)
> > [pid 18373] futex(0x2b76d0736a00, FUTEX_WAKE_PRIVATE, 1) = 0
> > [pid 18373] futex(0x2b76d0736a44,
> > 

Re: [gmx-users] Gromacs version for polarizable model

[Justin Lemkul]

On 6/22/16 3:11 AM, Luca Banetta wrote:

Dear all,
I am trying to use a polarizable model for acetone molecule. After
lots of attempts we created a stable model for a single acetone
molecule in a sea of water running the simulation on one core.
So then we started new simulations with a certain number of acetone
molecules and the simulation appeared to run, but unfortunately it
doesn't write anything in log file, xtc or trr files.



The SCF approach to doing polarizable simulations (the only thing supported in 
GROMACS until my Drude branch is ready for merge - I'm working out the last bug, 
hopefully) is VERY expensive.  Simulations can be orders of magnitude slower 
than comparable additive systems due to the many additional force calls that are 
required to relax the shells.  This gets exacerbated in the case of using only 
one core.


You can try increasing the simulation output (nstlog, nstxtcout, etc) to confirm 
that it's still running or use verbose mode (mdrun -v) to see the progress in 
real time.


-Justin


Is this a problema connected with an old version of the code (4.5.4)
that I used?
If yes, which code should I get?

In thw following lines I show:

TOPOLOGY

#include "oplsaaff.itp"
#include "oplsaa.ff/spc.itp"
[ moleculetype ]
; Namenrexcl
acetone  3

[ atoms ]
;   nr   type  resnr   residue  atom  cgnr
chargemass  typeBchargeBmassB
 1  opls_280 1   LIG C 1 -0.4712.011
 2  opls_135 1   LIG C 2 -0.1812.011
 3  opls_135 1   LIG C 3 -0.1812.011
 4  opls_281 1   LIG O 1  0.47
   15.5994
 5  opls_282 1   LIG H 2  0.06 1.008
 6  opls_282 1   LIG H 2  0.06 1.008
 7  opls_282 1   LIG H 2  0.06 1.008
 8  opls_282 1   LIG H 3  0.06 1.008
 9  opls_282 1   LIG H 3  0.06 1.008
10  opls_282 1   LIG H 3  0.06 1.008
11 SP1   LIG SP1 -0.47 0.400
12 VS1   LIG VS1  0.47 0.000

[ polarization ]
;   atom  shell   functiontype  alpha nm^3
  4 1110.001

[ bonds ]
;  aiaj functc0c1c2c3
1 2 1
1 3 1
1 4 1
112 6
2 5 1
2 6 1
2 7 1
212 6
3 8 1
3 9 1
310 1
312 6
411 1

[ pairs ]
;  aiaj functc0c1c2c3
2 8 1
2 9 1
210 1
3 5 1
3 6 1
3 7 1
4 5 1
4 6 1
4 7 1
4 8 1
4 9 1
410 1

[ angles ]
;  aiajak functc0c1c2c3
2 1 3 1
2 1 4 1
3 1 4 1
1 2 5 1
1 2 6 1
1 2 7 1
5 2 6 1
5 2 7 1
6 2 7 1
1 3 8 1
1 3 9 1
1 310 1
8 3 9 1
8 310 1
9 310 1

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
3 1 2 5 3
3 1 2 6 3
3 1 2 7 3
4 1 2 5 3
4 1 2 6 3
4 1 2 7 3
2 1 3 8 3
2 1 3 9 3
2 1 310 3
4 1 3 8 3
4 1 3 9 3
4 1 310 3

[ exclusions ]
; interazioni di non legame tra il primo atomo e i successivi non sono
considerate
1 2 3 4 5 6 7 8 9 10 11 12
2 3 4 5 6 7 8 9 10 11 12
3 4 5 6 7 8 9 10 11 12
4 5 6 7 8 9 10 11 12
5 6 7 8 9 10 11 12
6 7 8 9 10 11 12
7 8 9 10 11 12
8 9 10 11 12
9 10 11 12
10 11 12
11 12

[ virtual_sites2 ]
; site  ai  aj  funct   a
   12   1   41 -0.30


[ system ]
mixture

[ molecules ]
acetone 150
SOL1359

MDP FILE

; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  =
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.0001
nsteps   = 100
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of 

Re: [gmx-users] Block averaging

[Justin Lemkul]

On 6/22/16 5:02 AM, sun wrote:

Hello users and experts I have completed a 200 ns protein ligand simulation
using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational
change in protein in the presence of ligand and the results are as expected
and correlates to previous references as well. So, shall i believe that
simulation is converged or there is need to do block averaging over time
intervals? If block averaging is required, the parameters like RMSD and
propensities for secondary structure are sufficient to conclude that
simulation is converged? Or could anyone please tell me a suitable procedure
for making blocks and how to average those. With Regards Suniba



Just because a simulation produces expected results does not mean it is 
converged.  You must show that any quantities of interest from which you draw 
your conclusions, are not systematically varying with time.


-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] Gromacs tutorial similar to Justin Lemkul's

[Justin Lemkul]

On 6/21/16 8:10 PM, Roshan Shrestha wrote:

I am currently working on coarse-grain simulation of protein membrane. I am
about to finish Justin Lemkul's gromacs tutorial on KALP-15 in DPPC. Are
there any tutorials similar to KALP-15 or more advanced than KALP-15 which
I can work on after completing this tutorial ? Thanks



I have lots.  Whether or not they're useful depends on what you want to learn:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html

-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] amino acid on solid surface

[Mark Abraham]

Hi,

Why aren't you looking at distance between surface and adsorbant as a
criterion?

Mark

On Wed, Jun 22, 2016 at 11:24 AM Alexander Alexander <
alexanderwie...@gmail.com> wrote:

> Dear Gromacs user,
>
> I am simulating the adsorption behavior of single amino acid or a short
> peptide into a solid surface in water, after all the minimisation,
> equlibrsation, and production,  how should I find out if the amino acid has
> been absorbed?
>
> Does RMSD help? I calculated the RMSD for amino acid, its backbone and
> mainchain, respected to their minimized situations. Their RMSD crazily
> oscillate first for a while and then somewhere after 15 or 20 ns, they just
> ranging between 0.05 and 0.12. Do you think this means adsorption?
>
> Thanks.
> Best regards,
> Alex
> --
> Gromacs Users mailing list
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[gmx-users] amino acid on solid surface

[Alexander Alexander]

Dear Gromacs user,

I am simulating the adsorption behavior of single amino acid or a short
peptide into a solid surface in water, after all the minimisation,
equlibrsation, and production,  how should I find out if the amino acid has
been absorbed?

Does RMSD help? I calculated the RMSD for amino acid, its backbone and
mainchain, respected to their minimized situations. Their RMSD crazily
oscillate first for a while and then somewhere after 15 or 20 ns, they just
ranging between 0.05 and 0.12. Do you think this means adsorption?

Thanks.
Best regards,
Alex
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[gmx-users] Block averaging

[sun]

Hello users and experts
I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and 
Gromacs v 5.0. I expected to observe a conformational change in protein in the 
presence of ligand and the results are as expected and correlates to previous 
references as well. So, shall i believe that simulation is converged or there 
is need to do block averaging over time intervals? If block averaging is 
required, the parameters like RMSD and propensities for secondary structure are 
sufficient to conclude that simulation is converged? Or could anyone please 
tell me a suitable procedure for making blocks and how to average those. 
With Regards
Suniba

Sent from my iPhone
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Re: [gmx-users] Effect of pressure coupling time constant on equilibrium densities

[Mark Abraham]

Hi,

On Tue, Jun 21, 2016 at 4:47 PM Miguel Caro  wrote:

> Dear all,
>
> I am doing some NPT calculations for simple liquids and liquid mixtures.
> I have noticed that for water I can use small time constants for the
> pressure coupling (with the Berendsen barostat). However, for
> dimethylformamide, which is a larger molecule, my system "blows up" and
> I need to increase the tau_p value.
>

The molecular size and the need for tau_p to be from any particular range
of values should have no relationship. I'd be looking at your equilibration
protocol, constraints settings and timestep.

As I understand it, Berendsen does not correctly reproduce the pressure
> fluctuations that correspond to a canonical ensemble, however it is a
> quick and easy way to equilibrate a system's pressure. As a matter of
> fact, I had to switch to Berendsen after I encountered some problems
> with more sophisticated barostats. I only use Berendsen to obtain the
> right average density of my system, after which my production
> calculations are carried out within the NVT ensemble.
>

Fine, do that.


> If I understand it correctly, a small pressure time constant allows
> quicker (but also more abrupt and "blowing-up-prone") pressure
> equilibration than a large one, therefore having to increase this
> constant is suboptimal. My question is the following: how does the
> choice of pressure time constant for the Berendsen barostat affect (if
> at all) the *average equilibrium pressure* in a Gromacs simulation (as
> opposed to the *rate of convergence* or the *amplitude of pressure
> fluctuations*)?
>

It doesn't affect the equilibrium value, only the rate of approach to it
and the nature of the fluctuations around it.

I would also like to know whether I should expect Berendsen to yield an
> incorrect average density or only incorrect pressure fluctuations.
>

The average is correct, given your model of reality.

Mark


> Many thanks in advance,
> Miguel
> --
> *Dr. Miguel Caro*
> /Postdoctoral researcher/
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: *mcar...@gmail.com*
> Work: *miguel.c...@aalto.fi*
> Website: http://mcaroba.dyndns.org
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] Dielectric Constant

[Mark Abraham]

Hi,


On Tue, Jun 21, 2016 at 5:22 PM Life Sciences Inc <
contact.lifesciences@gmail.com> wrote:

> Hi
>
> I am getting the value of Epsilon from the output of gmx dipoles as
> approximately close to 60, in my mdp file I used the default parameters for
> epsilon-r (1) and for epsilon-rf(0), the output as below
>

These are totally different things - the resulting epsilon of your whole
simulation system, vs the effective dielectric of your model physics that
produces the simulation.

Clearly you haven't read the .mdp descriptions


> Select a group: 12
> Selected 12: 'Water'
> There are 4531 molecules in the selection
> Last frame  5 time 10.000
> Average volume over run is 149.579
>
> Dipole moment (Debye)
>  -
> Average  =   2.2740  Std. Dev. =   0.0001  Error =   0.
>
> The following averages for the complete trajectory have been calculated:
>
> Total < M_x > = 3.03347 Debye
> Total < M_y > = -12.361 Debye
> Total < M_z > = -19.1034 Debye
>
> Total < M_x^2 > = 28871.2 Debye^2
> Total < M_y^2 > = 29326.8 Debye^2
> Total < M_z^2 > = 29241.6 Debye^2
>
> Total < |M|^2 > = 87439.6 Debye^2
> Total |< M >|^2 = 526.935 Debye^2
>
> < |M|^2 > - |< M >|^2 = 86912.7 Debye^2
>
> Finite system Kirkwood g factor G_k = 3.7096
>
> Infinite system Kirkwood g factor g_k = 2.49376
>
> Epsilon = 59.7615
>
>
> But I want to calculate the dielectric constant with the imaginary surface
> around my system or it can also be said as with PBC boundaries, for which
> there is an option in gromacs for mdp file which is epsilon-surface(0), but
> whenever I am using this option with other than default value with
> epsilon-r = 1 or epsilon-rf = 0 or epsilon-r = 1 or epsilon-rf = 1,  I am
> getting LINCs error. For electrostatistics I am using PME.


Hmm, if you'd done what I already asked and checked the .mdp documentation,
then you'd know that varying epsilon-rf is useless with PME.
epsilon-surface could well be buggy (since it is not automatically tested),
but AFAICR it doesn't affect the forces, so your LINCS errors must have
some other origin - eg whatever ad hoc changes you are making to your model
physics.


> As I have used
> SPC water model I tried to use the value of epsilon-surface = 70, and also
> used 60 so that these values may correct the lincs error.


Why are those sensible values? Have you read the .mdp documentation for
what this means?

Mark


> I have also made
> my input molecule as a whole using gromacs. Simulation runs if I use
> epsilon-surface = 0 but other than this simulation i not running. I am
> using gromacs version 5.
>
> I am not getting where is the problem and how it can be solved.
>
> Kindly help.
>
> On Thu, Jun 16, 2016 at 10:05 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > These are all documented in the mdp sections. What isn't clear?
> >
> > Mark
> >
> > On Thu, 16 Jun 2016 18:06 Life Sciences Inc <
> > contact.lifesciences@gmail.com> wrote:
> >
> > > Hi all
> > >
> > > Exactly in Gromacs what and where is Dielectric constant option , If
> for
> > > example I have to run simulations to study behavior of water around
> > > molecules, and I am using experimental value of SPC/E water model as 71
> > for
> > > Dielectric constant. But in my input file for gromacs where I will put
> > > Dielectric constant is it epsilon-surface, or epsilon-r or
> epsisilon-rf,
> > it
> > > is little confusing. Kindly someone elaborate .
> > >
> > > Thank you
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
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> > > posting!
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> > >
> > --
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> >
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Re: [gmx-users] Gromacs version for polarizable model

[Mark Abraham]

Hi,

Don't know. Try 5.1.2.

Mark

On Wed, Jun 22, 2016 at 9:12 AM Luca Banetta  wrote:

> NNODES=1, MYRANK=0, HOSTNAME=compute-0-2.local
>  :-)  G  R  O  M  A  C  S  (-:
>
>Grunge ROck MAChoS
>
> :-)  VERSION 4.5.4  (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>Berk Hess, David van der Spoel, and Erik Lindahl.
>
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
> :-)  mdrun  (-:
>
> Option Filename  Type Description
> 
>   -s  topol.tpr  InputRun input file: tpr tpb tpa
>   -o   traj.trr  Output   Full precision trajectory: trr trj cpt
>   -x   traj.xtc  Output, Opt. Compressed trajectory (portable xdr
> format)
> -cpi  state.cpt  Input, Opt.  Checkpoint file
> -cpo  state.cpt  Output, Opt. Checkpoint file
>   -cconfout.gro  Output   Structure file: gro g96 pdb etc.
>   -e   ener.edr  Output   Energy file
>   -g md.log  Output   Log file
> -dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
> -fieldfield.xvg  Output, Opt. xvgr/xmgr file
> -tabletable.xvg  Input, Opt.  xvgr/xmgr file
> -tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
> -tableb   table.xvg  Input, Opt.  xvgr/xmgr file
> -rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
> -tpitpi.xvg  Output, Opt. xvgr/xmgr file
> -tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
>  -eisam.edi  Input, Opt.  ED sampling input
>  -eosam.edo  Output, Opt. ED sampling output
>   -j   wham.gct  Input, Opt.  General coupling stuff
>  -jobam.gct  Output, Opt. General coupling stuff
> -ffout  gct.xvg  Output, Opt. xvgr/xmgr file
> -devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
> -runav  runaver.xvg  Output, Opt. xvgr/xmgr file
>  -px  pullx.xvg  Output, Opt. xvgr/xmgr file
>  -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
> -mtx nm.mtx  Output, Opt. Hessian matrix
>  -dn dipole.ndx  Output, Opt. Index file
> -multidirrundir  Input, Opt., Mult. Run directory
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -[no]version bool   no  Print version info and quit
> -niceint0   Set the nicelevel
> -deffnm  string Set the default filename for all file options
> -xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -[no]pd  bool   no  Use particle decompostion
> -dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
> -npmeint-1  Number of separate nodes to be used for PME, -1
> is guess
> -ddorder enum   interleave  DD node order: interleave, pp_pme or
> cartesian
> -[no]ddcheck bool   yes Check for all bonded interactions with DD
> -rdd real   0   The maximum distance for bonded interactions
> with
> DD (nm), 0 is determine from initial
> coordinates
> -rconreal   0   Maximum distance for P-LINCS (nm), 0 is
> estimate
> -dlb enum   autoDynamic load balancing (with DD): auto, no or
> yes
> -dds real   0.8 Minimum allowed dlb scaling of the DD cell size
> -gcomint-1  Global communication frequency
> -[no]v   bool   no  Be loud and noisy
> -[no]compact bool   yes Write a compact log file
> -[no]seppot  bool   no  Write separate V and dVdl terms for each
> interaction type and node to the log file(s)
> -pforce  real   -1  Print all forces larger than this (kJ/mol nm)
> -[no]reprod  bool   no  Try to avoid optimizations that affect binary
> reproducibility
> -cpt real   15  Checkpoint interval (minutes)
> -[no]cpnum   bool   no  Keep and number checkpoint files
> -[no]append  bool   yes Append to previous output files when continuing
> 

Re: [gmx-users] Gromacs version for polarizable model

[Luca Banetta]

NNODES=1, MYRANK=0, HOSTNAME=compute-0-2.local
 :-)  G  R  O  M  A  C  S  (-:

   Grunge ROck MAChoS

:-)  VERSION 4.5.4  (-:

Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  mdrun  (-:

Option Filename  Type Description

  -s  topol.tpr  InputRun input file: tpr tpb tpa
  -o   traj.trr  Output   Full precision trajectory: trr trj cpt
  -x   traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -cconfout.gro  Output   Structure file: gro g96 pdb etc.
  -e   ener.edr  Output   Energy file
  -g md.log  Output   Log file
-dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file
-multidirrundir  Input, Opt., Mult. Run directory

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum   autoDynamic load balancing (with DD): auto, no or yes
-dds real   0.8 Minimum allowed dlb scaling of the DD cell size
-gcomint-1  Global communication frequency
-[no]v   bool   no  Be loud and noisy
-[no]compact bool   yes Write a compact log file
-[no]seppot  bool   no  Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce  real   -1  Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no  Try to avoid optimizations that affect binary
reproducibility
-cpt real   15  Checkpoint interval (minutes)
-[no]cpnum   bool   no  Keep and number checkpoint files
-[no]append  bool   yes Append to previous output files when continuing
from checkpoint instead of adding the simulation
part number to all file names
-maxhreal   -1  Terminate after 0.99 times this time (hours)
-multi   int0   Do multiple simulations in parallel
-replex  int0   

[gmx-users] Gromacs version for polarizable model

[Luca Banetta]

Dear all,
I am trying to use a polarizable model for acetone molecule. After
lots of attempts we created a stable model for a single acetone
molecule in a sea of water running the simulation on one core.
So then we started new simulations with a certain number of acetone
molecules and the simulation appeared to run, but unfortunately it
doesn't write anything in log file, xtc or trr files.

Is this a problema connected with an old version of the code (4.5.4)
that I used?
If yes, which code should I get?

In thw following lines I show:

TOPOLOGY

#include "oplsaaff.itp"
#include "oplsaa.ff/spc.itp"
[ moleculetype ]
; Namenrexcl
acetone  3

[ atoms ]
;   nr   type  resnr   residue  atom  cgnr
chargemass  typeBchargeBmassB
 1  opls_280 1   LIG C 1 -0.4712.011
 2  opls_135 1   LIG C 2 -0.1812.011
 3  opls_135 1   LIG C 3 -0.1812.011
 4  opls_281 1   LIG O 1  0.47
   15.5994
 5  opls_282 1   LIG H 2  0.06 1.008
 6  opls_282 1   LIG H 2  0.06 1.008
 7  opls_282 1   LIG H 2  0.06 1.008
 8  opls_282 1   LIG H 3  0.06 1.008
 9  opls_282 1   LIG H 3  0.06 1.008
10  opls_282 1   LIG H 3  0.06 1.008
11 SP1   LIG SP1 -0.47 0.400
12 VS1   LIG VS1  0.47 0.000

[ polarization ]
;   atom  shell   functiontype  alpha nm^3
  4 1110.001

[ bonds ]
;  aiaj functc0c1c2c3
1 2 1
1 3 1
1 4 1
112 6
2 5 1
2 6 1
2 7 1
212 6
3 8 1
3 9 1
310 1
312 6
411 1

[ pairs ]
;  aiaj functc0c1c2c3
2 8 1
2 9 1
210 1
3 5 1
3 6 1
3 7 1
4 5 1
4 6 1
4 7 1
4 8 1
4 9 1
410 1

[ angles ]
;  aiajak functc0c1c2c3
2 1 3 1
2 1 4 1
3 1 4 1
1 2 5 1
1 2 6 1
1 2 7 1
5 2 6 1
5 2 7 1
6 2 7 1
1 3 8 1
1 3 9 1
1 310 1
8 3 9 1
8 310 1
9 310 1

[ dihedrals ]
;  aiajakal functc0c1
c2c3c4c5
3 1 2 5 3
3 1 2 6 3
3 1 2 7 3
4 1 2 5 3
4 1 2 6 3
4 1 2 7 3
2 1 3 8 3
2 1 3 9 3
2 1 310 3
4 1 3 8 3
4 1 3 9 3
4 1 310 3

[ exclusions ]
; interazioni di non legame tra il primo atomo e i successivi non sono
considerate
1 2 3 4 5 6 7 8 9 10 11 12
2 3 4 5 6 7 8 9 10 11 12
3 4 5 6 7 8 9 10 11 12
4 5 6 7 8 9 10 11 12
5 6 7 8 9 10 11 12
6 7 8 9 10 11 12
7 8 9 10 11 12
8 9 10 11 12
9 10 11 12
10 11 12
11 12

[ virtual_sites2 ]
; site  ai  aj  funct   a
   12   1   41 -0.30


[ system ]
mixture

[ molecules ]
acetone 150
SOL1359

MDP FILE

; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  =
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.0001
nsteps   = 100
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=

; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
;ref-t= 300
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest 

Re: [gmx-users] Does gmx covar/gmx anaeig give or T for ligand binding?

[Billy Williams-Noonan]

Yes, still with two ligands...  So I assume that  should be halved to
about -0.25 kJ/mol K, which would give T= -75.

I found out recently that we have access to a node with 1TB of RAM.

So the solvent is still relevant?  If the amount of memory I need for the
entropy calculation is given by *( 3*N )^2 * 4 *where N is the number of
atoms, I should be able to calculate the entropy of systems (including
solvent) on that node.  If I have to multiply by the number of frames then
I can't.

Is the formula above correct?  Because according to it, with about 50,000
atoms in my system, I would need 90 GB of RAM, which is odd, because GMX
covar crashed when I used a node with 128GB RAM and one core.

Billy



On 22 June 2016 at 16:05, David van der Spoel  wrote:

> On 22/06/16 06:44, Billy Williams-Noonan wrote:
>
>>I re-did the calculation.  When considering the entire biomolecule of
>> each ensemble:
>>
>> ' = 51760 J/mol K
>>
>>  = 50640 J/mol K
>>
>>  = 814 J/mol K
>>
>>Resulting in = -0.51 kJ/mol K
>>
> Still with two ligands? This still corresponds to a binding entropy change
> of -150 kJ/mol. Of course you are ignoring the entropy change of the water
> which is probably almost the same magnitude and with opposite sign. If you
> want more quantitative results you could consider doing a PMF but your
> ligand is very large so that will be difficult to converge as well.
>
>
>
>>
>>And when just considering Protein-H, I got:
>>
>> ' = 31941 J/mol K
>>
>>  = 31340 J/mol K
>>
>>  = 640 J/mol K
>>
>>Resulting in = -0.69 kJ/mol K
>>
>>
>>These values make more sense given my enthalpy calculation with
>> g_mmpbsa
>> is likely not converged.  Thank you for your time and patience. :)
>>
>> Billy
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On 22 June 2016 at 13:40, Billy Williams-Noonan <
>> billy.williams-noo...@monash.edu> wrote:
>>
>> Sorry that was the ATB, not the ATP
>>>
>>> On 22 June 2016 at 13:39, Billy Williams-Noonan <
>>> billy.williams-noo...@monash.edu> wrote:
>>>
>>> Hi David,

   Thanks again for responding... Sorry if I came across the wrong way.
 I'm not trying to disprove the code, but simply understand why my values
 don't make sense  I trust your knowledge on this subject too, since I
 suspect you're one of the geniuses who helped to develop
 g_covar/g_anaeig.
 :)  I know the units for entropy too.

   I should explain that I have previously performed relative FEP
 calculations of ligands binding to the site of interest, and reproduced
 experimental binding affinities within 1.4 kcal/mol of experiment.
 Ligand
 topologies came from the ATP using a GROMOS united atom force-field.
 So I
 know that the protocol I use for system equilibration is working.

Using the same equilibration protocol as with the FEP protocol, and
 having tried an absolute FEP calculation with restraints that failed
 dismally, I have a cyclic peptide that has mM affinity for the same
 binding
 site as the aforementioned ligands (see above paragraph).  So, using the
 same protein as a model and placing the cyclic peptide in the correct
 orientation as determined by the crystal structure, I am trying to use
 g_mmpbsa to get an absolute binding affinity.  Of course the entropic
 term
 from the g_mmpbsa calculation is missing, so I am using g_covar and
 g_anaeig to determine the entropy.

You're right about the size of my ligand too of course.  The cyclic
 peptide is 54 atoms in size and moves quite a lot in solution.  I am
 used a
 Parrinello-Rahman/V-rescale NPT ensemble, set to 300K and 1 bar, for the
 entirety of the 100ns simulation.  And my protein is a symmetrical dimer
 (two of the same protein bound to each other) so there is one ligand for
 each monomer, forming 108 atoms between the two ligands.

When I initially made this thread, the variables I was talking about
 were:

  = 128,886 J/mol/K
 = Entropy of one ligand bound to one side of the protein dimer,
 despite another ligand being bound on the other side.  a_1-3071 was
 selected (twice) in g covar to represent the P.L complex, despite there
 being 3125 atoms in total

  = 153,548 J/mol/K
 = Entropy of the protein

  = 4137 J/mol/K
 = Entropy of the cyclic peptide

So I redefined , as ', and selected a_1-3125 this
 morning, to get the entropy of the dimer complexed with two cyclic
 peptides, and got a value of 51,759.8 J/mol/K.  I substituted this into
 the
 equation (1)

  = ' -  - 2*  --(1)

I multiplied the entropy of the ligand by two to account for the fact
 that the beginning state now has the two ligands and the protein in
 solution, while the end state 

Re: [gmx-users] Does gmx covar/gmx anaeig give or T for ligand binding?

[David van der Spoel]

On 22/06/16 06:44, Billy Williams-Noonan wrote:

   I re-did the calculation.  When considering the entire biomolecule of
each ensemble:

' = 51760 J/mol K

 = 50640 J/mol K

 = 814 J/mol K

   Resulting in = -0.51 kJ/mol K
Still with two ligands? This still corresponds to a binding entropy 
change of -150 kJ/mol. Of course you are ignoring the entropy change of 
the water which is probably almost the same magnitude and with opposite 
sign. If you want more quantitative results you could consider doing a 
PMF but your ligand is very large so that will be difficult to converge 
as well.






   And when just considering Protein-H, I got:

' = 31941 J/mol K

 = 31340 J/mol K

 = 640 J/mol K

   Resulting in = -0.69 kJ/mol K


   These values make more sense given my enthalpy calculation with g_mmpbsa
is likely not converged.  Thank you for your time and patience. :)

Billy









On 22 June 2016 at 13:40, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:


Sorry that was the ATB, not the ATP

On 22 June 2016 at 13:39, Billy Williams-Noonan <
billy.williams-noo...@monash.edu> wrote:


Hi David,

  Thanks again for responding... Sorry if I came across the wrong way.
I'm not trying to disprove the code, but simply understand why my values
don't make sense  I trust your knowledge on this subject too, since I
suspect you're one of the geniuses who helped to develop g_covar/g_anaeig.
:)  I know the units for entropy too.

  I should explain that I have previously performed relative FEP
calculations of ligands binding to the site of interest, and reproduced
experimental binding affinities within 1.4 kcal/mol of experiment.  Ligand
topologies came from the ATP using a GROMOS united atom force-field.  So I
know that the protocol I use for system equilibration is working.

   Using the same equilibration protocol as with the FEP protocol, and
having tried an absolute FEP calculation with restraints that failed
dismally, I have a cyclic peptide that has mM affinity for the same binding
site as the aforementioned ligands (see above paragraph).  So, using the
same protein as a model and placing the cyclic peptide in the correct
orientation as determined by the crystal structure, I am trying to use
g_mmpbsa to get an absolute binding affinity.  Of course the entropic term
from the g_mmpbsa calculation is missing, so I am using g_covar and
g_anaeig to determine the entropy.

   You're right about the size of my ligand too of course.  The cyclic
peptide is 54 atoms in size and moves quite a lot in solution.  I am used a
Parrinello-Rahman/V-rescale NPT ensemble, set to 300K and 1 bar, for the
entirety of the 100ns simulation.  And my protein is a symmetrical dimer
(two of the same protein bound to each other) so there is one ligand for
each monomer, forming 108 atoms between the two ligands.

   When I initially made this thread, the variables I was talking about
were:

 = 128,886 J/mol/K
= Entropy of one ligand bound to one side of the protein dimer,
despite another ligand being bound on the other side.  a_1-3071 was
selected (twice) in g covar to represent the P.L complex, despite there
being 3125 atoms in total

 = 153,548 J/mol/K
= Entropy of the protein

 = 4137 J/mol/K
= Entropy of the cyclic peptide

   So I redefined , as ', and selected a_1-3125 this
morning, to get the entropy of the dimer complexed with two cyclic
peptides, and got a value of 51,759.8 J/mol/K.  I substituted this into the
equation (1)

 = ' -  - 2*  --(1)

   I multiplied the entropy of the ligand by two to account for the fact
that the beginning state now has the two ligands and the protein in
solution, while the end state has the protein dimer complexed with those
two ligands. And, the answer was -110.072 kJ/mol/K.

   So I am clearly doing something wrong and I'd like some advice on what
it is...  I doubt it's an equilibration problem, since my FEP calculations
previously worked with the same equilibration protocol.  And I doubt this
is a convergence issue too, since a  this high should prohibit binding
in most cases, and my ligand definitely binds as seen by viewing the
complex simulation on VMD.

   Advice? Thoughts?  I am about to try it with just the Protein-H atoms
from the index files to see if that changes anything...

Billy

On 21 June 2016 at 21:51, David van der Spoel 
wrote:


On 21/06/16 11:26, Billy Williams-Noonan wrote:


Hi Gromacs Users,

  I have used gmx covar and gmx anaeig to generate three ensemble
average
entropies over 100ns: first for a ligand in solution (), second
for a
protein in solution () and third for their respective complex in
solution ().

   My understanding is that the change in entropy upon binding is given
by:

 =  -  -    ---(1)

   Using gmx covar/gmx anaeig I got Quasi-Harmonic entropy estimates