date:20160209

Hi,

On Sun, Feb 7, 2016 at 8:00 PM Johannes Wagner 
wrote:

> hey guys,
> came across an issue with pp/pme ratio difference from 5.0 to 5.1. For a
> system running on 2 nodes with a pp/pme ratio of 80:16 on 5.0, the same
> thing starts with 72:24 on gromacs 5.1. The 5.1 run has a much higher load
> imbalance and is hence slower. Are there known changes from 5.0 to 5.1 in
> the pp/pme ratio that cause this?
>

Yes and no. Even on only two nodes, your observations can be affected by
network congestion, so I would investigate whether you can reproduce the
observations. The changes that I identified that had the capacity to change
performance are noted at
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/performance.html.
For example, if you're using LINCS then the SIMD improvements there affect
only the PP ranks so it might seem to the auto-tuner that it's more
efficient to use fewer PP ranks. Then later some kind of load imbalance has
a stronger effect. The interactions of DD DLB and PME tuning are complex,
and we can't rule out that there's a problem that we should fix. But we
can't say much without being able to compare some (reproducible) log files.

Mark

cheers, johannes
>
> --
> 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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Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

2016-02-09 Thread Dries Van Rompaey

Hi Mark,

Thanks for the clarification. I did use the rerun option as described in
the link you provided.
I uploaded my log files here:
https://www.dropbox.com/sh/tcmqhn5fszeis27/AABcYOI6_FrjG7qoYJycf_35a?dl=0

Thanks for your time,
Kind regards

Dries

On 9 February 2016 at 09:20, Mark Abraham  wrote:

> Hi,
>
> On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey <
> dries.vanromp...@gmail.com>
> wrote:
>
> > Hi,
> >
> > The corresponding mdp output section is:
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype  = PME
> > coulomb-modifier = Potential-shift-Verlet
> > rcoulomb-switch  = 0
> > rcoulomb = 1.0
> > ; Relative dielectric constant for the medium and the reaction field
> > epsilon-r= 1
> > epsilon-rf   = 0
> > ; Method for doing Van der Waals
> > vdwtype  = cutoff
> > vdw-modifier = Potential-switch
> > ; cut-off lengths
> > rvdw-switch  = 0.9
> > rvdw = 1.0
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr = EnerPres
> > ; Extension of the potential lookup tables beyond the cut-off
> > table-extension  = 1
> > ; Separate tables between energy group pairs
> > energygrp-table  =
> > ; Spacing for the PME/PPPM FFT grid
> > fourierspacing   = 0.08
> > ; FFT grid size, when a value is 0 fourierspacing will be used
> > fourier-nx   = 0
> > fourier-ny   = 0
> > fourier-nz   = 0
> > ; EWALD/PME/PPPM parameters
> > pme_order= 6
> > ewald_rtol   = 1e-06
> > ewald-rtol-lj= 0.001
> > lj-pme-comb-rule = Geometric
> > ewald-geometry   = 3d
> > epsilon_surface  = 0
>
>
> That all seems reasonable.
>
>
> > I evaluated the energy with:
> >
> > Verlet - settings above (with standard verlet-buffer-tolerance)
> > @ s0 legend "Coulomb-14"
> > @ s1 legend "Coulomb (SR)"
> > @ s2 legend "Coul. recip."
> > 0.00  -2221.295898  -546205.25  9271.518555
> > Total - 539155.0273
> >
> > Verlet - settings above - with verlet-buffer-tolerance -1
> > 0.00  -2221.295898  -546205.25  9271.516602
> > Total   -539155.029296
> >
>
> That kind of agreement is expected, but perhaps might agree exactly if you
> were following
> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> Group - settings above
> > @ s0 legend "Coulomb-14"
> > @ s1 legend "Coulomb (SR)"
> > @ s2 legend "Coul. recip."
> > 0.00  -2221.296387  -487993.593750  -48931.437500
> > Total -539146.3276
> >
>
> The difference in those components is expected - in PME you have to avoid
> counting contributions in the long-range part from pairs that are excluded
> e.g. from the bonded topology. The two schemes handle this in different
> places. Their sum should match (within the limits of floating-point
> arithmetic), and a relative error under 1e-5 for summing a few million
> numbers is acceptable for judging the equivalence of the implementations.
>
> Verlet - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
> > @ s0 legend "Coulomb-14"
> > @ s1 legend "Coulomb (SR)"
> > 0.00  -2221.295898  -774817.875000
> > Total -777039.1709
> >
> >
> > Group - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
> > @ s0 legend "Coulomb-14"
> > @ s1 legend "Coulomb (SR)"
> > 0.00  -2221.296387  -553398.125000
> > Total -555619.4214
> >
>
> That ought to agree much better, but It's hard to speculate on where the
> problem lies without seeing log files. Please upload some to a file sharing
> service and post the links here (list doesn't take attachments)
>
> Mark
>
>
> > Thanks,
> >
> > Dries
> >
> > On 4 February 2016 at 14:48, Michael Shirts  wrote:
> >
> > > Also, can you be more precise about the inconsistency in the outputs
> > > you are seeing (with numerical output from GROMACS and analysis code).
> > >
> > > On Thu, Feb 4, 2016 at 6:17 AM, Michael Shirts 
> > wrote:
> > > > Hi, Dries-
> > > >
> > > > Can you print out what the corresponding section of mdout.mdp look
> > like?
> > > >
> > > > Have you  tried using the cutoffs above with group cutoffs, and seen
> > > > what the difference is?
> > > >
> > > > On Thu, Feb 4, 2016 at 4:59 AM, Dries Van Rompaey
> > > >  wrote:
> > > >> Hi,
> > > >>
> > > >> I'm using PME with the default Potential-Shift-Verlet modifier. If
> I'm
> > > >> interpreting the manual and comments on the mailinglist correctly,
> the
> > > >> settings for rcoulomb-switch shouldn't affect this and PME-switching
> > > >> shouldn't be necessary (although there seems to have been some
> > > discussion
> > > >> about this, https://gerrit.gromacs.org/#/c/2220/). Has a consensus
> > been
> > > >> reached elsewhere?
> > > >>
> > > >> Current nonbonded settings in

Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

Hi,

On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey 
wrote:

> Hi,
>
> The corresponding mdp output section is:
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = PME
> coulomb-modifier = Potential-shift-Verlet
> rcoulomb-switch  = 0
> rcoulomb = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r= 1
> epsilon-rf   = 0
> ; Method for doing Van der Waals
> vdwtype  = cutoff
> vdw-modifier = Potential-switch
> ; cut-off lengths
> rvdw-switch  = 0.9
> rvdw = 1.0
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Separate tables between energy group pairs
> energygrp-table  =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.08
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier-nx   = 0
> fourier-ny   = 0
> fourier-nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 6
> ewald_rtol   = 1e-06
> ewald-rtol-lj= 0.001
> lj-pme-comb-rule = Geometric
> ewald-geometry   = 3d
> epsilon_surface  = 0


That all seems reasonable.


> I evaluated the energy with:
>
> Verlet - settings above (with standard verlet-buffer-tolerance)
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> @ s2 legend "Coul. recip."
> 0.00  -2221.295898  -546205.25  9271.518555
> Total - 539155.0273
>
> Verlet - settings above - with verlet-buffer-tolerance -1
> 0.00  -2221.295898  -546205.25  9271.516602
> Total   -539155.029296
>

That kind of agreement is expected, but perhaps might agree exactly if you
were following
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Group - settings above
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> @ s2 legend "Coul. recip."
> 0.00  -2221.296387  -487993.593750  -48931.437500
> Total -539146.3276
>

The difference in those components is expected - in PME you have to avoid
counting contributions in the long-range part from pairs that are excluded
e.g. from the bonded topology. The two schemes handle this in different
places. Their sum should match (within the limits of floating-point
arithmetic), and a relative error under 1e-5 for summing a few million
numbers is acceptable for judging the equivalence of the implementations.

Verlet - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> 0.00  -2221.295898  -774817.875000
> Total -777039.1709
>
>
> Group - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
> @ s0 legend "Coulomb-14"
> @ s1 legend "Coulomb (SR)"
> 0.00  -2221.296387  -553398.125000
> Total -555619.4214
>

That ought to agree much better, but It's hard to speculate on where the
problem lies without seeing log files. Please upload some to a file sharing
service and post the links here (list doesn't take attachments)

Mark


> Thanks,
>
> Dries
>
> On 4 February 2016 at 14:48, Michael Shirts  wrote:
>
> > Also, can you be more precise about the inconsistency in the outputs
> > you are seeing (with numerical output from GROMACS and analysis code).
> >
> > On Thu, Feb 4, 2016 at 6:17 AM, Michael Shirts 
> wrote:
> > > Hi, Dries-
> > >
> > > Can you print out what the corresponding section of mdout.mdp look
> like?
> > >
> > > Have you  tried using the cutoffs above with group cutoffs, and seen
> > > what the difference is?
> > >
> > > On Thu, Feb 4, 2016 at 4:59 AM, Dries Van Rompaey
> > >  wrote:
> > >> Hi,
> > >>
> > >> I'm using PME with the default Potential-Shift-Verlet modifier. If I'm
> > >> interpreting the manual and comments on the mailinglist correctly, the
> > >> settings for rcoulomb-switch shouldn't affect this and PME-switching
> > >> shouldn't be necessary (although there seems to have been some
> > discussion
> > >> about this, https://gerrit.gromacs.org/#/c/2220/). Has a consensus
> been
> > >> reached elsewhere?
> > >>
> > >> Current nonbonded settings in my .mdp files are:
> > >> ; Electrostatics
> > >> coulombtype  = PME
> > >> rcoulomb= 1.0
> > >>
> > >> ; van der Waals
> > >> vdwtype= cutoff
> > >> vdw-modifier= Potential-switch
> > >> rvdw-switch  = 0.9
> > >> rvdw = 1.0
> > >>
> > >> ; Apply long range dispersion corrections for Energy and Pressure
> > >> DispCorr  = EnerPres
> > >>
> > >> ; Spacing for the PME/PPPM FFT grid
> > >> fourierspacing   = 0.08
> > >>
> > >> ; EWALD/PME/PPPM parameters
> > >>

[gmx-users] Fw: wrong number of control atomes in hdb



--- On Tue, 9/2/16, Mehreen Jan  wrote:

> From: Mehreen Jan 
> Subject: wrong number of control atomes  in  hdb
> To: "Mehreen Jan" 
> Received: Tuesday, 9 February, 2016, 2:44 PM
> 
> 
> On Tue, 9/2/16, Mehreen Jan 
> wrote:
> 
>  Subject: Re: gromacs.org_gmx-users Digest, Vol 142, Issue
> 42
>  To: gromacs.org_gmx-users@maillist.sys.kth.se
>  Received: Tuesday, 9 February, 2016, 2:43 PM
>  
>   Subject: Fw: wrong number of control
>  atomes in
>  > hdb
>  > >
>  
>  
>  > > > > respected sir!
>  > > > > thank you for advise
>  > > > >
>  > > > > thank you sir for advise i just copy
>  folder
>  > 43A1p
>  > > and
>  > > > past
>  > > > > in top file and in GMXLIB and it work
>  error
>  > is
>  > > solved
>  > > > know
>  > > > > after running the command:
>  > > > >  pdb2gmx -f protein.top -o
>  protein.gro
>  > > > > select the forcefield 43A1p the
>  following
>  > error
>  > > is
>  > > > occurs
>  > > > > i google it but i can't get it exactly
>  and i
>  > read
>  > > > manual but
>  > > > > difficult to understand because of 
>  no
>  > experience
>  > > .
>  > > > > respected sir kiendle find the
>  attachment .
>  > > > >
>  > > > >    
>  > > > > error in hdb file
>  > ./gromacs43A1p/aminoacid.hdb:
>  > > > >
>  > > > > wrong number of control atoms (2 iso3)
>  on
>  > line:
>  > > > > 2 3 N -C -CA
>  
>  On Tue, 9/2/16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>  
>  wrote:
>  
>   Subject: gromacs.org_gmx-users Digest, Vol 142, Issue
> 42
>   To: gromacs.org_gmx-users@maillist.sys.kth.se
>   Received: Tuesday, 9 February, 2016, 1:20 PM
>   
>   Send gromacs.org_gmx-users mailing
>   list submissions to
>       gromacs.org_gmx-users@maillist.sys.kth.se
>   
>   To subscribe or unsubscribe via the World Wide Web,
> visit
>       https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>   or, via email, send a message with subject or body
> 'help'
>   to
>       gromacs.org_gmx-users-requ...@maillist.sys.kth.se
>   
>   You can reach the person managing the list at
>       gromacs.org_gmx-users-ow...@maillist.sys.kth.se
>   
>   When replying, please edit your Subject line so it is
> more
>   specific
>   than "Re: Contents of gromacs.org_gmx-users
> digest..."
>   
>   
>   Today's Topics:
>   
>      1. Different results for same protein's
>   simulation in    4.6.5 and
>         5.0.4 (SAPNA BORAH)
>      2. Re: Different results for same
>   protein's simulation in 4.6.5
>         and 5.0.4 (Mark Abraham)
>      3. Re: creating representative structures
>   (Mark Abraham)
>      4. Re: pp/pme ratio differences between
>   gromacs 5.0.x and    5.1.x
>         (Mark Abraham)
>      5. Re: Fwd: FW: PME settings in free
>   energy calculations
>         (Mark Abraham)
>   
>   
>  
> --
>   
>   Message: 1
>   Date: Tue, 9 Feb 2016 12:52:41 +0530
>   From: SAPNA BORAH 
>   To: gmx-us...@gromacs.org
>   Subject: [gmx-users] Different results for same
> protein's
>   simulation
>       in    4.6.5 and 5.0.4
>   Message-ID:
>       
>   Content-Type: text/plain; charset=UTF-8
>   
>   Dear all,
>   
>   I have tried running the same protein in the two
> versions
>  of
>   gromacs 4.6.5
>   and 5.0.4. Now, both the runs are producing entirely
>   different results.
>   
>   The results till equilibration are same.
>   
>   After the run however, there is a total change in
> the
>   production results. I
>   have used the same mdp files.
>   
>   I have rerun the systems and they still produce
> similar
>   results in the same
>   version.
>   
>   The protein structure is a modelled one.
>   
>   
>   Thanks in advance.
>   Sapna.
>   
>   Sapna Mayuri Borah
>   c/o Dr. A. N. Jha
>   Research student
>   Tezpur University,
>   India
>   
>   
>   --
>   
>   Message: 2
>   Date: Tue, 09 Feb 2016 07:37:54 +
>   From: Mark Abraham 
>   To: gmx-us...@gromacs.org
>   Subject: Re: [gmx-users] Different results for same
>   protein's
>       simulation in 4.6.5 and 5.0.4
>   Message-ID:
>      
>   
>   Content-Type: text/plain; charset=UTF-8
>   
>   Hi,
>   
>   This is quite normal.
>  
> http://www.gromacs.org/Documentation/Terminology/Reproducibility.
>   You
>   should see a similar range of variation in the
>  trajectories
>   produced in the
>   two versions that are incompletely sampling the same
>   ensemble, but one can
>   say very little about two single observed
> trajectories
>   sampled from them.
>   
>   Mark
>   
>   On Tue, Feb 9, 2016 at

Re: [gmx-users] pp/pme ratio differences between gromacs 5.0.x and 5.1.x

2016-02-09 Thread Johannes Wagner

thanks, I will look a bit deeper into this! My last reply can then be 
disregarded.

Johannes

> On 9 Feb  2016, at 9:20 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
> wrote:
> 
>> hey guys,
>> came across an issue with pp/pme ratio difference from 5.0 to 5.1. For a
>> system running on 2 nodes with a pp/pme ratio of 80:16 on 5.0, the same
>> thing starts with 72:24 on gromacs 5.1. The 5.1 run has a much higher load
>> imbalance and is hence slower. Are there known changes from 5.0 to 5.1 in
>> the pp/pme ratio that cause this?
>> cheers, johannes
>> 
> 
> Yes and no. Even on only two nodes, your observations can be affected by
> network congestion, so I would investigate whether you can reproduce the
> observations. The changes that I identified that had the capacity to change
> performance are noted at
> http://manual.gromacs.org/documentation/5.1/ReleaseNotes/performance.html 
> .
> For example, if you're using LINCS then the SIMD improvements there affect
> only the PP ranks so it might seem to the auto-tuner that it's more
> efficient to use fewer PP ranks. Then later some kind of load imbalance has
> a stronger effect. The interactions of DD DLB and PME tuning are complex,
> and we can't rule out that there's a problem that we should fix. But we
> can't say much without being able to compare some (reproducible) log files.
> 
> Mark

-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 42

 Subject: Fw: wrong number of control atomes in
> hdb
> >

> > > > respected sir!
> > > > thank you for advise
> > > >
> > > > thank you sir for advise i just copy folder
> 43A1p
> > and
> > > past
> > > > in top file and in GMXLIB and it work error
> is
> > solved
> > > know
> > > > after running the command:
> > > >  pdb2gmx -f protein.top -o protein.gro
> > > > select the forcefield 43A1p the following
> error
> > is
> > > occurs
> > > > i google it but i can't get it exactly and i
> read
> > > manual but
> > > > difficult to understand because of  no
> experience
> > .
> > > > respected sir kiendle find the attachment .
> > > >
> > > >
> > > > error in hdb file
> ./gromacs43A1p/aminoacid.hdb:
> > > >
> > > > wrong number of control atoms (2 iso3) on
> line:
> > > > 2 3 N -C -CA

On Tue, 9/2/16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
 wrote:

 Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 42
 To: gromacs.org_gmx-users@maillist.sys.kth.se
 Received: Tuesday, 9 February, 2016, 1:20 PM

 Send gromacs.org_gmx-users mailing
 list submissions to
     gromacs.org_gmx-users@maillist.sys.kth.se

 To subscribe or unsubscribe via the World Wide Web, visit
     https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or, via email, send a message with subject or body 'help'
 to
     gromacs.org_gmx-users-requ...@maillist.sys.kth.se

 You can reach the person managing the list at
     gromacs.org_gmx-users-ow...@maillist.sys.kth.se

 When replying, please edit your Subject line so it is more
 specific
 than "Re: Contents of gromacs.org_gmx-users digest..."

 Today's Topics:

    1. Different results for same protein's
 simulation in    4.6.5 and
       5.0.4 (SAPNA BORAH)
    2. Re: Different results for same
 protein's simulation in 4.6.5
       and 5.0.4 (Mark Abraham)
    3. Re: creating representative structures
 (Mark Abraham)
    4. Re: pp/pme ratio differences between
 gromacs 5.0.x and    5.1.x
       (Mark Abraham)
    5. Re: Fwd: FW: PME settings in free
 energy calculations
       (Mark Abraham)

 --

 Message: 1
 Date: Tue, 9 Feb 2016 12:52:41 +0530
 From: SAPNA BORAH 
 To: gmx-us...@gromacs.org
 Subject: [gmx-users] Different results for same protein's
 simulation
     in    4.6.5 and 5.0.4
 Message-ID:

 Content-Type: text/plain; charset=UTF-8

 Dear all,

 I have tried running the same protein in the two versions of
 gromacs 4.6.5
 and 5.0.4. Now, both the runs are producing entirely
 different results.

 The results till equilibration are same.

 After the run however, there is a total change in the
 production results. I
 have used the same mdp files.

 I have rerun the systems and they still produce similar
 results in the same
 version.

 The protein structure is a modelled one.

 Thanks in advance.
 Sapna.

 Sapna Mayuri Borah
 c/o Dr. A. N. Jha
 Research student
 Tezpur University,
 India

 --

 Message: 2
 Date: Tue, 09 Feb 2016 07:37:54 +
 From: Mark Abraham 
 To: gmx-us...@gromacs.org
 Subject: Re: [gmx-users] Different results for same
 protein's
     simulation in 4.6.5 and 5.0.4
 Message-ID:

 Content-Type: text/plain; charset=UTF-8

 Hi,

 This is quite normal.
 http://www.gromacs.org/Documentation/Terminology/Reproducibility.
 You
 should see a similar range of variation in the trajectories
 produced in the
 two versions that are incompletely sampling the same
 ensemble, but one can
 say very little about two single observed trajectories
 sampled from them.

 Mark

 On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH 
 wrote:

 > Dear all,
 >
 > I have tried running the same protein in the two
 versions of gromacs 4.6.5
 > and 5.0.4. Now, both the runs are producing entirely
 different results.
 >
 > The results till equilibration are same.
 >
 > After the run however, there is a total change in the
 production results. I
 > have used the same mdp files.
 >
 > I have rerun the systems and they still produce similar
 results in the same
 > version.
 >
 > The protein structure is a modelled one.
 >
 >
 > Thanks in advance.
 > Sapna.
 >
 > Sapna Mayuri Borah
 > c/o Dr. A. N. Jha
 > Research student
 > Tezpur University,
 > India
 > --
 > 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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 > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
 > send a mail to gmx-users-requ...@gromacs.org.
 >

Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

Hi,

Runs 2 and 3 are using different rvdw and rvdw-switch, which doesn't seem
like the comparison you should want to make. However that should not affect
the Coulomb calculation at all - and certainly not to this degree. What do
you see when it matches? I notice that somehow you are triggering the use
of the generic nonbonded kernel - is that deliberate by you?

The group scheme plus rvdw != rcoulomb plus a switch could well be a
combination that got broken at some point. I tried to verify such
equivalence before we released 5.0, but I could well have missed some. If
so, the rerun with 4.5.7 would be instructive. (Michael's advice on
alchemistry.org is largely based on 4.5-era GROMACS).

Mark

On Tue, Feb 9, 2016 at 9:51 AM Dries Van Rompaey 
wrote:

> Hi Mark,
>
> Thanks for the clarification. I did use the rerun option as described in
> the link you provided.
> I uploaded my log files here:
> https://www.dropbox.com/sh/tcmqhn5fszeis27/AABcYOI6_FrjG7qoYJycf_35a?dl=0
>
> Thanks for your time,
> Kind regards
>
> Dries
>
> On 9 February 2016 at 09:20, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey <
> > dries.vanromp...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > The corresponding mdp output section is:
> > >
> > > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > > ; Method for doing electrostatics
> > > coulombtype  = PME
> > > coulomb-modifier = Potential-shift-Verlet
> > > rcoulomb-switch  = 0
> > > rcoulomb = 1.0
> > > ; Relative dielectric constant for the medium and the reaction field
> > > epsilon-r= 1
> > > epsilon-rf   = 0
> > > ; Method for doing Van der Waals
> > > vdwtype  = cutoff
> > > vdw-modifier = Potential-switch
> > > ; cut-off lengths
> > > rvdw-switch  = 0.9
> > > rvdw = 1.0
> > > ; Apply long range dispersion corrections for Energy and Pressure
> > > DispCorr = EnerPres
> > > ; Extension of the potential lookup tables beyond the cut-off
> > > table-extension  = 1
> > > ; Separate tables between energy group pairs
> > > energygrp-table  =
> > > ; Spacing for the PME/PPPM FFT grid
> > > fourierspacing   = 0.08
> > > ; FFT grid size, when a value is 0 fourierspacing will be used
> > > fourier-nx   = 0
> > > fourier-ny   = 0
> > > fourier-nz   = 0
> > > ; EWALD/PME/PPPM parameters
> > > pme_order= 6
> > > ewald_rtol   = 1e-06
> > > ewald-rtol-lj= 0.001
> > > lj-pme-comb-rule = Geometric
> > > ewald-geometry   = 3d
> > > epsilon_surface  = 0
> >
> >
> > That all seems reasonable.
> >
> >
> > > I evaluated the energy with:
> > >
> > > Verlet - settings above (with standard verlet-buffer-tolerance)
> > > @ s0 legend "Coulomb-14"
> > > @ s1 legend "Coulomb (SR)"
> > > @ s2 legend "Coul. recip."
> > > 0.00  -2221.295898  -546205.25  9271.518555
> > > Total - 539155.0273
> > >
> > > Verlet - settings above - with verlet-buffer-tolerance -1
> > > 0.00  -2221.295898  -546205.25  9271.516602
> > > Total   -539155.029296
> > >
> >
> > That kind of agreement is expected, but perhaps might agree exactly if
> you
> > were following
> > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> >
> > Group - settings above
> > > @ s0 legend "Coulomb-14"
> > > @ s1 legend "Coulomb (SR)"
> > > @ s2 legend "Coul. recip."
> > > 0.00  -2221.296387  -487993.593750  -48931.437500
> > > Total -539146.3276
> > >
> >
> > The difference in those components is expected - in PME you have to avoid
> > counting contributions in the long-range part from pairs that are
> excluded
> > e.g. from the bonded topology. The two schemes handle this in different
> > places. Their sum should match (within the limits of floating-point
> > arithmetic), and a relative error under 1e-5 for summing a few million
> > numbers is acceptable for judging the equivalence of the implementations.
> >
> > Verlet - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
> > > @ s0 legend "Coulomb-14"
> > > @ s1 legend "Coulomb (SR)"
> > > 0.00  -2221.295898  -774817.875000
> > > Total -777039.1709
> > >
> > >
> > > Group - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
> > > @ s0 legend "Coulomb-14"
> > > @ s1 legend "Coulomb (SR)"
> > > 0.00  -2221.296387  -553398.125000
> > > Total -555619.4214
> > >
> >
> > That ought to agree much better, but It's hard to speculate on where the
> > problem lies without seeing log files. Please upload some to a file
> sharing
> > service and post the links here (list doesn't take attachments)
> >
> > Mark
> >
> >
> > > Thanks,
> > >
> > > Dries
> > >
> > > On 4 February 2016 at 14:48, Michael Shirts 
> wrote:
> > >
> > > > Also, can you be more precise about the

[gmx-users] wrong number of control atoms (2 iso 3) on line: 2 3 N -C -CA

gromacs4.5.5
phosphorylated protein - protein-protein interaction
phosphate at  "SEP" and TPO
forcefield 43A1p download from gromacs web page
command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro

fatal error:
error in hdb file ./gromos43A1p.ff/aminoacid.hdb
wrong number of control atoms (2 iso 3) on line:
2 3 N -C -CA
i read manual but i can't remove error.  i did not get the point how to remove 
error

HDB file s given:


ABU 1   
11HN-CCA
ACEH1   
34HACACO
AIB 1   
11HN-CCA
ALA 1   
11HN-CCA
ARG 4   
11HN-CCA
11HENECDCZ
23HH1NH1CZNE
23HH2NH2CZNE
ARGN4   
11HN-CCA
11HENECDCZ
12HH1NH1CZNE
23HH2NH2CZNE
ASN 2   
11HN-CCA
23HD2ND2CGCB
ASP 1   
11HN-CCA
ASP12   
11HN-CCA
12HD1OD1CGCB
ASPH2   
11HN-CCA
12HD2OD2CGCB
BEN 7   
11H2C2C1C3
11H3C3C2C4
11H4C4C3C5
11H5C5C4C6
11H6C6C5C1
23H1N1C7C1
23H2N2C7C1
CYS21   
11HN-CCA
CYSH2   
11HN-CCA
12HGSGCBCA
FAD 7   
23HN6AN6AC6AC5
12HO2*AO2*AC2*AC1*
12HO3*AO3*AC3*AC2*
12H4*O4*C4*C5*
12H3*O3*C3*C4*
12H2*O2*C2*C3*
12H3N3C4C4A
GLN 2   
11HN-CCA
23HE2NE2CDCG
GLU 1   
11HN-CCA
GLUH2   
11HN-CCA
12HE2OE2CDCG
GLY 1   
11HN-CCA
HEME4   
11HHACHAC1AC4D
11HHBCHBC1BC4A
11HHCCHCC1CC4B
11HHDCHDC1DC4C
HIS12   
11HN-CCA
11HD1ND1CGCE1
HISA2   
11HN-CCA
11HD1ND1CGCE1
HISB2   
11HN-CCA
11HE2NE2CE1CD2
HISH3   
11HN-CCA
11HD1ND1CGCE1
11HE2NE2CE1CD2
HO4 1   
310HWOW
HOH 1   
27HWOW
HYP 1   
12HD1OD1CGCB
ILE 1   
11HN-CCA
LEU 1   
11HN-CCA
LYS 2   
11HN-CCA
24HZNZCECD
LYSH2   
11HN-CCA
34HZNZCECD
MET 1   
11HN-CCA
NAC 1   
11HN-CCA
NACH2   
11HN-CCA
34HACANNH
NH2 1   
23HN-C-CA
PHE 6   
11HN-CCA
11HD1CD1CGCE1
11HD2CD2CGCE2
11HE1CE1CD1CZ
11HE2CE2CD2CZ
11HZCZCE1CE2
PHEU1   
11HN-CCA
PHL 7   
11HN-CCA
11HD1CD1CGCE1
11HD2CD2CGCE2
11HE1CE1CD1CZ
11HE2CE2CD2CZ
11HZCZCE1CE2
12HYOYCXCA
SER 2   
11HN-CCA
12HGOGCBCA
TFE 1   
12HOCH2C
THR 2   
11HN-CCA
12HG1OG1CBCA
TRP 7   
11HN-CCA
11HD1CD1CGNE1
11HE1NE1CD1CE2
11HE3CE3CD2CZ3
11HZ3CZ3CE3CH2
11HH2CH2CZ3CZ2
11HZ2CZ2CE2CH2
TRPU2   
11HN-CCA
11HE1NE1CD1CE2
TYR 6   
11HN-CCA
11HD1CD1CGCE1
11HD2CD2CGCE2
11HE1CE1CD1CZ
11HE2CE2CD2CZ
12HHOHCZCE1
TYRU2   
11HN-CCA
12HHOHCZCE1
VAL 1   
11HN-CCA
SEP 1
1   1   HN   -C  CA
TPO 1
1   1   HN   -C  CA
PTR 5
1   1   HN   -C  CA
1   1   HD1CD1 CG  CE1
1   1   HD2CD2 CG  CE2
1   1   HE1CE1 CD1 CZ
1   1   HE2CE2 CD2 CZ
SEPH2
1   1   HN   -C  CA
1   2   H3PO3P  P  OG
TPOH2
1   1   HN   -C

Re: [gmx-users] pp/pme ratio differences between gromacs 5.0.x and 5.1.x

2016-02-09 Thread Johannes Wagner

yes, that reproduces the performance. Of course I can always manually fine-tune 
pp/pme ratio. It’s just that gromacs 5.0 gave a quite good out of the box 
pp/pme ratio that allowed to submit the same job with [x] more nodes without 
thinking about it much. Now it seems we always needs to test for each change in 
run parameters. Be it box size, number of nodes, different queue with different 
core configuration. And thats what my question was, if it is intended behavior 
that gromacs 5.1 does estimate the pp/pme ratio in a different way than gromacs 
5.0 for an identical system.

Johannes

> Hi,
> 
> you could try to manually set the number of PME nodes with -npme in 5.1.
> Does that reproduce the 5.0 performance?
> 
> Carsten
> 
> 
>> On 07 Feb 2016, at 19:57, Johannes Wagner > > wrote:
>> 
>> hey guys,
>> came across an issue with pp/pme ratio difference from 5.0 to 5.1. For a 
>> system running on 2 nodes with a pp/pme ratio of 80:16 on 5.0, the same 
>> thing starts with 72:24 on gromacs 5.1. The 5.1 run has a much higher load 
>> imbalance and is hence slower. Are there known changes from 5.0 to 5.1 in 
>> the pp/pme ratio that cause this?
>> 
>> cheers, johannes
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Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

2016-02-09 Thread Dries Van Rompaey

Hi Mark,

Thanks for your pointers. The energies obtained with a shifted potential
match up a lot better.

Kind regards

Dries

On 9 February 2016 at 14:30, Mark Abraham  wrote:

> Hi,
>
> On Tue, Feb 9, 2016 at 1:30 PM Dries Van Rompaey <
> dries.vanromp...@gmail.com>
> wrote:
>
> > Hi,
> >
> > I'm not deliberately triggering the generic kernel.
>
>
> OK, well that means its a setup that we have deliberately not tried to make
> fast in the group scheme, because it's too hard to do for the expected
> usefulness.
>
>
> > I unfortunately have no
> > idea what's causing that. I uploaded logfiles for a setup with matching
> > cutoffs as setup3alt and setup2alt (I got quite a lot of warnings for
> this
> > setup, which is why I initially changed the cutoffs slightly).
> >
> > I'm a bit baffled what could cause the large difference between the
> verlet
> > setup with long cutoffs and the verlet setup with shorter cutoffs and
> PME..
> > After all, that's the one that should be fairly close in order to prove
> my
> > electrostatics treatment is appropriate. This difference seems to be a
> lot
> > more pronounced than the difference to the group scheme.
> >
>
> That's the easy one. You're comparing potentials from Verlet PME with a
> short-ranged potential shift with Verlet plain cutoffs with no potential
> shift. The shift is quite small with PME (that's what ewald-rtol is all
> about) but it applies to every single in-range interaction. Your
> long-cutoff calculation has a cutoff that is only ~3 times longer than the
> modified short-ranged form you used with PME. That increase in range is not
> going to get down to 1e-5 relative error from truncation at the cutoff, and
> it also applies to a lot more interactions. I expect that this is
> confounding all your comparisons with Verlet+PME - you need to compare with
> a scheme with a potential shift. (This also leads people astray when they
> are e.g. comparing total energies between GROMACS and codes that don't use
> the potential shift.)
>
> Whether such comparisons as alchemistry.org suggests worked reasonably
> well
> with Group+PME vs Group+long-cutoff (because neither used a potential
> shift) with current or old code, I don't know.
>
> Mark
> --
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Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

Hi,

On Tue, Feb 9, 2016 at 1:30 PM Dries Van Rompaey 
wrote:

> Hi,
>
> I'm not deliberately triggering the generic kernel.

OK, well that means its a setup that we have deliberately not tried to make
fast in the group scheme, because it's too hard to do for the expected
usefulness.

> I unfortunately have no
> idea what's causing that. I uploaded logfiles for a setup with matching
> cutoffs as setup3alt and setup2alt (I got quite a lot of warnings for this
> setup, which is why I initially changed the cutoffs slightly).
>
> I'm a bit baffled what could cause the large difference between the verlet
> setup with long cutoffs and the verlet setup with shorter cutoffs and PME..
> After all, that's the one that should be fairly close in order to prove my
> electrostatics treatment is appropriate. This difference seems to be a lot
> more pronounced than the difference to the group scheme.
>

That's the easy one. You're comparing potentials from Verlet PME with a
short-ranged potential shift with Verlet plain cutoffs with no potential
shift. The shift is quite small with PME (that's what ewald-rtol is all
about) but it applies to every single in-range interaction. Your
long-cutoff calculation has a cutoff that is only ~3 times longer than the
modified short-ranged form you used with PME. That increase in range is not
going to get down to 1e-5 relative error from truncation at the cutoff, and
it also applies to a lot more interactions. I expect that this is
confounding all your comparisons with Verlet+PME - you need to compare with
a scheme with a potential shift. (This also leads people astray when they
are e.g. comparing total energies between GROMACS and codes that don't use
the potential shift.)

Whether such comparisons as alchemistry.org suggests worked reasonably well
with Group+PME vs Group+long-cutoff (because neither used a potential
shift) with current or old code, I don't know.

Mark
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Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

2016-02-09 Thread Dries Van Rompaey

Hi,

I'm not deliberately triggering the generic kernel. I unfortunately have no
idea what's causing that. I uploaded logfiles for a setup with matching
cutoffs as setup3alt and setup2alt (I got quite a lot of warnings for this
setup, which is why I initially changed the cutoffs slightly).

I'm a bit baffled what could cause the large difference between the verlet
setup with long cutoffs and the verlet setup with shorter cutoffs and PME..
After all, that's the one that should be fairly close in order to prove my
electrostatics treatment is appropriate. This difference seems to be a lot
more pronounced than the difference to the group scheme.

Thanks,

Dries

On 9 February 2016 at 11:06, Mark Abraham  wrote:

> Hi,
>
> Runs 2 and 3 are using different rvdw and rvdw-switch, which doesn't seem
> like the comparison you should want to make. However that should not affect
> the Coulomb calculation at all - and certainly not to this degree. What do
> you see when it matches? I notice that somehow you are triggering the use
> of the generic nonbonded kernel - is that deliberate by you?
>
> The group scheme plus rvdw != rcoulomb plus a switch could well be a
> combination that got broken at some point. I tried to verify such
> equivalence before we released 5.0, but I could well have missed some. If
> so, the rerun with 4.5.7 would be instructive. (Michael's advice on
> alchemistry.org is largely based on 4.5-era GROMACS).
>
> Mark
>
> On Tue, Feb 9, 2016 at 9:51 AM Dries Van Rompaey <
> dries.vanromp...@gmail.com>
> wrote:
>
> > Hi Mark,
> >
> > Thanks for the clarification. I did use the rerun option as described in
> > the link you provided.
> > I uploaded my log files here:
> >
> https://www.dropbox.com/sh/tcmqhn5fszeis27/AABcYOI6_FrjG7qoYJycf_35a?dl=0
> >
> > Thanks for your time,
> > Kind regards
> >
> > Dries
> >
> > On 9 February 2016 at 09:20, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey <
> > > dries.vanromp...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > The corresponding mdp output section is:
> > > >
> > > > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > > > ; Method for doing electrostatics
> > > > coulombtype  = PME
> > > > coulomb-modifier = Potential-shift-Verlet
> > > > rcoulomb-switch  = 0
> > > > rcoulomb = 1.0
> > > > ; Relative dielectric constant for the medium and the reaction field
> > > > epsilon-r= 1
> > > > epsilon-rf   = 0
> > > > ; Method for doing Van der Waals
> > > > vdwtype  = cutoff
> > > > vdw-modifier = Potential-switch
> > > > ; cut-off lengths
> > > > rvdw-switch  = 0.9
> > > > rvdw = 1.0
> > > > ; Apply long range dispersion corrections for Energy and Pressure
> > > > DispCorr = EnerPres
> > > > ; Extension of the potential lookup tables beyond the cut-off
> > > > table-extension  = 1
> > > > ; Separate tables between energy group pairs
> > > > energygrp-table  =
> > > > ; Spacing for the PME/PPPM FFT grid
> > > > fourierspacing   = 0.08
> > > > ; FFT grid size, when a value is 0 fourierspacing will be used
> > > > fourier-nx   = 0
> > > > fourier-ny   = 0
> > > > fourier-nz   = 0
> > > > ; EWALD/PME/PPPM parameters
> > > > pme_order= 6
> > > > ewald_rtol   = 1e-06
> > > > ewald-rtol-lj= 0.001
> > > > lj-pme-comb-rule = Geometric
> > > > ewald-geometry   = 3d
> > > > epsilon_surface  = 0
> > >
> > >
> > > That all seems reasonable.
> > >
> > >
> > > > I evaluated the energy with:
> > > >
> > > > Verlet - settings above (with standard verlet-buffer-tolerance)
> > > > @ s0 legend "Coulomb-14"
> > > > @ s1 legend "Coulomb (SR)"
> > > > @ s2 legend "Coul. recip."
> > > > 0.00  -2221.295898  -546205.25  9271.518555
> > > > Total - 539155.0273
> > > >
> > > > Verlet - settings above - with verlet-buffer-tolerance -1
> > > > 0.00  -2221.295898  -546205.25  9271.516602
> > > > Total   -539155.029296
> > > >
> > >
> > > That kind of agreement is expected, but perhaps might agree exactly if
> > you
> > > were following
> > > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> > >
> > > Group - settings above
> > > > @ s0 legend "Coulomb-14"
> > > > @ s1 legend "Coulomb (SR)"
> > > > @ s2 legend "Coul. recip."
> > > > 0.00  -2221.296387  -487993.593750  -48931.437500
> > > > Total -539146.3276
> > > >
> > >
> > > The difference in those components is expected - in PME you have to
> avoid
> > > counting contributions in the long-range part from pairs that are
> > excluded
> > > e.g. from the bonded topology. The two schemes handle this in different
> > > places. Their sum should match (within the limits of floating-point
> > > arithmetic), and a relative

[gmx-users] Getting and keeping ACPYPE updated

2016-02-09 Thread Alan

Hi everyone,

Many thanks for those who helped for, used or are interested in ACPYPE.

Since Google Code is now archived and, at University of Cambridge, it has
moved), the right way to get it now is by:

svn checkout
http://svn.code.sf.net/p/ccpn/code/branches/stable/ccpn/python/acpype acpype

Thanks,

Alan

-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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[gmx-users] complex topology file

2016-02-09 Thread Sana Saeed

 hi gmx usersi want to find out absolute binding free energy of protein ligand 
complex. fisrt i performed docking and selected best poses and then i made 
topology file of ligand with PRODRGserver. and then included itp file of ligand 
in Protein topology file (from pdb2gmx) , also made complex.gro as in tutorial 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
  . can i use these complex files for MD for absolute binding free energy? in 
some tutorials the topology file of complex is quite differently organised. 
please guide me, i am following decoupling and coupling steps from  
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate 
Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, 
South Korea.
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[gmx-users] add parameter

2016-02-09 Thread Mahnaz Mirsoltani

Hi
 I want to add some bond parameters in ffbonded.itp file, and
as I read in manual, unit of "kb" is "kj.mol-1.nm-2" and
 unit of "b0" is "nm". But I have these quantities with
 "kcal.mol-1.Å-2" and "Å". How do I convert these? Is it
enough converting of kcal/mol to kj/mol for "kb" and "Å" to
 'nm" for "b0"? 
 Thanks
 Mah
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[gmx-users] difference between gmx energy and gmx traj

2016-02-09 Thread Ray Chao

Hi, All,

I ran a NVT simulation for a water sphere with position restraint. The
TIP4P water model was used. I tried to relax the system at temperature of
300K.  After the simulation, I used gmx energy to cal the system
temperature and it is around 300K. However, when I tried to use gmx traj to
extract the temperature from "SOL" group, the temperature is always half of
that calculated from gmx energy. Is there any difference between these two
commands? Or is there any other way to determine the temperature of each
group?

Thank you very much.

Best regards,
Lei Zhao
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[gmx-users] Fw: add parameter

2016-02-09 Thread Mahnaz Mirsoltani

--- On Wed, 2/10/16, Mahnaz Mirsoltani  wrote:

> From: Mahnaz Mirsoltani 
> Subject: add parameter
> To: gmx-us...@gromacs.org
> Date: Wednesday, February 10, 2016, 1:14 AM
> Hi
> I want to add some bond parameters in ffbonded.itp file, and
> as I read in manual, unit of "kb" is "kj.mol-1.nm-2" and
> unit of "b0" is "nm". But I have these quantities with
> "kcal.mol-1.Å-2" and "Å". How do I convert these? Is it
> enough converting of kcal/mol to kj/mol for "kb" and "Å" to
> 'nm" for "b0"? 
> Thanks
> Mah
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Re: [gmx-users] difference between gmx energy and gmx traj




On 2/9/16 5:24 PM, Ray Chao wrote:

Hi, All,

I ran a NVT simulation for a water sphere with position restraint. The
TIP4P water model was used. I tried to relax the system at temperature of
300K.  After the simulation, I used gmx energy to cal the system
temperature and it is around 300K. However, when I tried to use gmx traj to
extract the temperature from "SOL" group, the temperature is always half of
that calculated from gmx energy. Is there any difference between these two
commands? Or is there any other way to determine the temperature of each
group?



You need to account for constraints.  See the help text of gmx traj and previous 
discussions on this topic in the archive.


-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] wrong number of control atoms (2 iso 3) on line: 2 3 N -C -CA



Please don't reply to the entire digest.  If you want to ask a new question, 
just send a new message to the mailing list.


On 2/9/16 5:34 AM, Mehreen Jan wrote:

gromacs4.5.5
phosphorylated protein - protein-protein interaction
phosphate at  "SEP" and TPO
forcefield 43A1p download from gromacs web page
command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro

fatal error:
error in hdb file ./gromos43A1p.ff/aminoacid.hdb
wrong number of control atoms (2 iso 3) on line:
2 3 N -C -CA
i read manual but i can't remove error.  i did not get the point how to remove 
error

HDB file s given:



There is no line in this file that would trigger that error.  Make sure you're 
looking at, and trying to use, the right files.


-Justin



ABU 1
11HN-CCA
ACEH1
34HACACO
AIB 1
11HN-CCA
ALA 1
11HN-CCA
ARG 4
11HN-CCA
11HENECDCZ
23HH1NH1CZNE
23HH2NH2CZNE
ARGN4
11HN-CCA
11HENECDCZ
12HH1NH1CZNE
23HH2NH2CZNE
ASN 2
11HN-CCA
23HD2ND2CGCB
ASP 1
11HN-CCA
ASP12
11HN-CCA
12HD1OD1CGCB
ASPH2
11HN-CCA
12HD2OD2CGCB
BEN 7
11H2C2C1C3
11H3C3C2C4
11H4C4C3C5
11H5C5C4C6
11H6C6C5C1
23H1N1C7C1
23H2N2C7C1
CYS21
11HN-CCA
CYSH2
11HN-CCA
12HGSGCBCA
FAD 7
23HN6AN6AC6AC5
12HO2*AO2*AC2*AC1*
12HO3*AO3*AC3*AC2*
12H4*O4*C4*C5*
12H3*O3*C3*C4*
12H2*O2*C2*C3*
12H3N3C4C4A
GLN 2
11HN-CCA
23HE2NE2CDCG
GLU 1
11HN-CCA
GLUH2
11HN-CCA
12HE2OE2CDCG
GLY 1
11HN-CCA
HEME4
11HHACHAC1AC4D
11HHBCHBC1BC4A
11HHCCHCC1CC4B
11HHDCHDC1DC4C
HIS12
11HN-CCA
11HD1ND1CGCE1
HISA2
11HN-CCA
11HD1ND1CGCE1
HISB2
11HN-CCA
11HE2NE2CE1CD2
HISH3
11HN-CCA
11HD1ND1CGCE1
11HE2NE2CE1CD2
HO4 1
310HWOW
HOH 1
27HWOW
HYP 1
12HD1OD1CGCB
ILE 1
11HN-CCA
LEU 1
11HN-CCA
LYS 2
11HN-CCA
24HZNZCECD
LYSH2
11HN-CCA
34HZNZCECD
MET 1
11HN-CCA
NAC 1
11HN-CCA
NACH2
11HN-CCA
34HACANNH
NH2 1
23HN-C-CA
PHE 6
11HN-CCA
11HD1CD1CGCE1
11HD2CD2CGCE2
11HE1CE1CD1CZ
11HE2CE2CD2CZ
11HZCZCE1CE2
PHEU1
11HN-CCA
PHL 7
11HN-CCA
11HD1CD1CGCE1
11HD2CD2CGCE2
11HE1CE1CD1CZ
11HE2CE2CD2CZ
11HZCZCE1CE2
12HYOYCXCA
SER 2
11HN-CCA
12HGOGCBCA
TFE 1
12HOCH2C
THR 2
11HN-CCA
12HG1OG1CBCA
TRP 7
11HN-CCA
11HD1CD1CGNE1
11HE1NE1CD1CE2
11HE3CE3CD2CZ3
11HZ3CZ3CE3CH2
11HH2CH2CZ3CZ2
11HZ2CZ2CE2CH2
TRPU2
11HN-CCA
11HE1NE1CD1CE2
TYR 6
11HN-CCA
11HD1CD1CGCE1
11HD2CD2CGCE2
11HE1CE1CD1CZ
11HE2CE2CD2CZ
12HHOHCZCE1
TYRU2
11HN-CCA
12HHOHCZCE1
VAL 1
11HN-CCA
SEP 1
1   1   HN   -C  CA
TPO 1
1   1   HN   -C  CA
PTR 5
1   1   HN   -C  CA
1   1   HD1CD1 CG  CE1
1   1   HD2CD2 CG  CE2
1   1   HE1CE1 CD1 CZ
1   1   HE2CE2 CD2 CZ
SEPH2
1   1   HN   -C  CA
1   2   H3PO3P  P  OG
TPOH2
1   1   HN   -C  CA

Re: [gmx-users] complex topology file

On 2/9/16 10:54 AM, Sana Saeed wrote:

hi gmx usersi want to find out absolute binding free energy of protein ligand
complex. fisrt i performed docking and selected best poses and then i made
topology file of ligand with PRODRGserver. and then included itp file of
ligand in Protein topology file (from pdb2gmx) , also made complex.gro as in
tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
. can i use these complex files for MD for absolute binding free energy? in
some tutorials the topology file of complex is quite differently organised.
please guide me, i am following decoupling and coupling steps from
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme

PRODRG topologies are inaccurate for even simple MD simulations. Using it for a
free energy calculation is certain to result in junk.

-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] what is control atoms???

thank you sir!
what is  control atoms in gromacs???how can we define  control atoms???
reason of control atom

On Wed, 10/2/16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
 wrote:

 Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 48
 To: gromacs.org_gmx-users@maillist.sys.kth.se
 Received: Wednesday, 10 February, 2016, 7:27 AM
 
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 Today's Topics:
 
    1. difference between gmx energy and gmx
 traj (Ray Chao)
    2. Re: wrong number of control atoms (2
 iso 3) on line: 2 3 N -C
       -CA (Justin Lemkul)
    3. Re: complex topology file (Justin
 Lemkul)
    4. Re: difference between gmx energy and
 gmx traj (Justin Lemkul)
    5. Re: add parameter (Justin Lemkul)
 
 
 --
 
 Message: 1
 Date: Tue, 9 Feb 2016 17:24:42 -0500
 From: Ray Chao 
 To: gmx-us...@gromacs.org
 Subject: [gmx-users] difference between gmx energy and gmx
 traj
 Message-ID:

[gmx-users] Gromacs installation FTP issue

2016-02-09 Thread Ragothaman Yennamalli

Hi Everyone,

I am trying to install the latest version of Gromacs. Before, I mention the
real question I have to let you know that our system admin has diabled FTP
downloads. (Don't ask me why, but all FTP usages in the campus are banned)
So, thanks to a Chrome extension I was able to download the gromacs
installation package using the browser.
However, while installing I realized that Gromcas tried to download the
regression tests package via FTP and it was unable to the installation was
unsuccessful. I have downloaded the regressiontests package from the
browser and trying to install it again.

So, my question is: Can I install Gromacs by bypassign FTP downloads?

Thanks for any input!

Raghu
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Re: [gmx-users] add parameter