Re: [gmx-users] COMPASS force field revisited Bond Dihedral and Angle Dihedral cross terms

[Broadbent, Richard]

On 21/02/2012 19:02, "David van der Spoel"  wrote:

> On 2/21/12 6:17 PM, Richard Broadbent wrote:
>> Dear All,
>> 
>> I am considering conducting a simulation of a polymeric system in
>> gromacs. I would like to use the COMPASS forcefield as it has a complete
>> parameter set for my molecule.
>> 
>> I believe the majority of the implementation is simple (though long and
>> fiddly). However, it has Bond-Dihedral and Angle-Dihedral cross terms.
>> These terms are not listed in either Chapter 4 or 5 of the Manual. Which
>> leads me to believe that they are not implemented. However CMAP
>> dihedrals are not documented in chapters 4&  5 and they are implemented
>> in the code. I therefore had a quick look in src/gmxlib/ifunc.c and
>> couldn't see those terms. However, my knowledge of the layout of the
>> source code is extremely limited so I could be looking in the wrong
>> place, and thought it best to ask.
>> 
>> Are Bond-Dihedral and Angle-Dihedral cross terms available in gromacs
>> 4.5.5?
> 
> What do the functions look like?
> 
Bond dihedral:
(b-b0)*[k_1*cos(phi) +k_2*cos(2*phi)+k_3*cos(3*phi)]

Angle Dihedral:
(theta -theta_0)*[k_1*cos(phi) +k_2*cos(2*phi)+k_3*cos(3*phi)]

There is also angle-angle-dihedral:
k*(theta -theta_0)*(theta' -theta_0')*cos(phi)

> Most likely they are not implemented though if they're not in the manual.

> 
>> 
>> 
>> Thanks,
>> 
>> Richard
>> 
> 

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Re: [gmx-users] How to read in mdcrd files to gromacs?

[Broadbent, Richard]

Dear Cat,

> Dear experts,
> 
> I am trying to do the following command:
> 
> /usr/local/gromacs/bin/g_covar_d -s test.pdb -f test.mdcrd -o -v
> 
If you are using -o & -v options you should specify files for them

> But the following error message is found:
> 
> ---
> Program g_covar_d, VERSION 4.5.5
> Source code file: trxio.c, line: 870
> 
> Fatal error:
> Not supported in read_first_frame: md0.mdcrd
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> What should I do next to solve this problem, I heard GROMACS can read mdcrd
> trajectory files from AMBER, right?
It can via VMD plugins:
http://www.gromacs.org/Documentation/How-tos/Using_VMD_plugins_to_read_traje
ctory_formats_not_native_to_GROMACS

Hope that's helpful

Richard
> 
> Best regards,
> 
> Cat
> 
>
> 
> 

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RE: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

[Broadbent, Richard]

Dear Marcelo,

I think you need to calm down. You are using a very nice piece of free code 
which has in excellent documentation as well as being open source.

If you are using a piece of software in a non-standard way it stands to reason 
that it might not be documented.  When this occurs in my research I simply run 
some test cases so that I can understand what is going on, or I refer to the 
source code which is available for all to see. These two approaches allow you 
to understand everything about how Gromacs functions. 

I do not know what your problem in the context of pair potential interactions 
in Gromacs is as you have failed to give any details, and therefore did not 
respond. Those who did respond directed you to sources of information which you 
ignored. 

The users of this mailing list and the Gromacs developers give up their time to 
assist others, insulting any of them is very offensive. 

Yours Sincerely,

Richard Broadbent







-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Marcelo Lopez
Sent: 07 May 2012 10:39
To: Discussion list for GROMACS users
Subject: Fwd: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?

You didn't reply the part where I told "unless you're trying to have some 
advantage"...


-- Forwarded message --
From: Mark Abraham 
Date: 2012/5/6
Subject: Re: [gmx-users] How to build 1-4 pairs tables for -tablep in mdrun?
To: Discussion list for GROMACS users 


On 7/05/2012 5:50 AM, Marcelo Lopez wrote:
>
> For sure, this wouldn't happened if the information to run all the 
> Gromacs features were clearly explained in the place where should be:
> the manual.


Life would be good if everything was perfect, but when you're relying on free 
software provided by largely volunteer effort, you have to accept some 
imperfections.


> Next time save some words and use your time to do a better 
> documentation job... unless you're trying to have some advantage...


You started these requests by asserting that no documentation existed.
So various people who might have helped you were probably annoyed and decided 
not to give time to you. However, you got pointed to a likely source of 
information. You seem to have ignored that. Eventually I got bored of ignoring 
your repeated requests and pointed you in the right direction again. Others 
have made worthwhile suggestions, but as far as we know you're ignoring them, 
too. Your frustration with solving your problem is understandable, but your 
assumption that you are entitled to perfect free software and to abuse those 
who help produce it is not understandable.

Mark


> Cheers!
>
> 2012/5/5 Mark Abraham:
>>
>> On 5/05/2012 11:39 PM, Marcelo Lopez wrote:
>>>
>>> Hi, all, I'm still confused about how to set up 1-4 interaction 
>>> tables for tabulated non-bonding potentials when using the -tablep 
>>> option in mdrun.
>>> The specific question is:
>>>
>>> How must I specify the 1-4 interaction in those tables? How many 
>>> columns and with what?
>>
>>
>> I suggested places to look for this information in answer to this 
>> question more than a week ago.
>> http://lists.gromacs.org/pipermail/gmx-users/2012-April/070856.html 
>> Your reply addressed only another part of the discussion. Why are you 
>> asking the same question again without appearing to have used the 
>> help you've been given?
>>
>>
>>> My primary goal is to set all the 1-4 interactions equal to zero. I 
>>> have some 1-4 pairs that aren't involved in dihedrals, that means 
>>> that setting up
>>>
>>> nrexcl = 3
>>>
>>> and
>>>
>>> gen-pairs = no
>>>
>>> isn't enough
>>
>>
>> In what sense? I suggested in that thread that you look at the 
>> contents of the .log files to see if any Coulomb 1-4 interactions 
>> exist, but you've not replied. Bald assertions that something doesn't 
>> work are likely to get people who might help to assume that the most 
>> likely explanation is that you're doing something wrong.
>>
>> Mark
>>
>> --
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Re: [gmx-users] compiling on different architecture than the compute nodes architecture

[Broadbent, Richard]

Dear Silard,

cmake -DGMX_CPU_ACCELERATION=AVX_256 -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX="_avx"  -DGMX_OPENMP=ON  -DGMX_MPI=ON -DGMX_DOUBLE=ON
-DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_FFT_LIBRARY=mkl
-DMKL_INCLUDE_DIR=$MKLROOT/include
-DMKL_LIBRARIES="$MKLROOT/lib/intel64/libmkl_core.so;$MKLROOT/lib/intel64/l
ibmkl_intel_lp64.so;$MKLROOT/lib/intel64/libmkl_sequential.so"
-DCMAKE_INSTALL_PREFIX=$HOME/libs/gromacs

Compiled, linked and installed without warning using intel-suite/2013,
mpi/intel-3.1, and cmake/2.8.9 I was compiling release-4-6 out of the git
repository ( 06935659a3125d9b44b84c57e67cb6788fda42c1 ). The job using
that executable is still in the queue, however, another one built using
the sse2 kernels ran a minimisation on a single core without problems.

How much faster fftw3 is than mkl for gromacs, is the difference likely to
be on the scale of 1-2% or 10%?

Thanks,

Richard


On 07/02/2013 02:17, "Szilárd Páll"  wrote:

>On Wed, Feb 6, 2013 at 6:03 PM, Richard Broadbent <
>richard.broadben...@imperial.ac.uk> wrote:
>
>> Dear All,
>>
>> I would like to compile gromacs 4.6 to run with the correct acceleration
>> on the compute nodes on our local cluster. Some of the nodes have intel
>> sandy-bridge whilst others only have sse4.1 and some (including the
>>login
>> and single core job nodes) are still stuck on ssse3 (gmx would use sse2
>> acceleration here).
>>
>> Installing several versions is not a problem however, I'm not sure how
>>to
>> make cmake build a version of the code that is not using the
>>acceleration
>> for the system on which the code is being compiled. Restrictions on job
>> sizes makes running the compilation on the sandy-bridge nodes almost
>> impossible. Can anyone let me know which flags cmake needs to enable
>> avx-256 acceleration?
>>
>> my standard cmake line is:
>>
>> $ CC=mpiicc CXX=mpiicpc ; cmake -DGMX_OPENMP=ON  -DGMX_MPI=ON
>> -DGMX_DOUBLE=ON -DGMX_GPU=OFF -DGMX_PREFER_STATIC_LIBS=ON
>> -DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR=$MKLROOT/**include
>> -DMKL_LIBRARIES="$MKLROOT/lib/**intel64/libmkl_core.so;$**
>> 
>>MKLROOT/lib/intel64/libmkl_**intel_lp64.so;$MKLROOT/lib/**intel64/libmkl_
>>sequential.so"
>> -DCMAKE_INSTALL_PREFIX=$HOME/**libs/gromacs  ../
>>
>
>Note that MKL (without the fftw wrappers) is known to not work out of the
>box. Making it work requires a fairly simple workaround described here:
>http://redmine.gromacs.org/issues/1110#note-3
>
>Additionally, note that FFTW is in most cases faster than MKL (but if you
>find the contrary do let us know).
>
>--
>Szilárd
>
>
>
>>
>>
>>
>> Thanks,
>>
>> Richard
>> --
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>> 
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Re: [gmx-users] Bond potential of atom groups

[Broadbent, Richard]

Dear Steven,

There is no universal method to do this and many people spend years
studying the various techniques. However,
http://pubs.acs.org/doi/abs/10.1021/ct900369w gives an overview of some of
the most widespread techniques used and its references will provide
further details. Futhermore, the VOTCA code it describes (www.votca.org)
provides tools for building such potentials and is compatible with gromacs
file formats.

Regards,

Richard

On 13/02/2013 16:07, "Steven Neumann"  wrote:

>Dear Gmx Users,
>
>I want to create coarse grained model. I need bond constant and
>equilibrium distance according to the equation
>
>V(r) =K (R - Req)^2
>
>I wish to extract bonded potential between beads made out 3 atoms. I
>need Req and K. Equilibrium distance is straight forward - g_dist
>between COM or COG with index file conatining those 3 atoms. To match
>force constant K  I need to extract bonded potential and try to fit to
>my parabolic curve.
>
>My question:
>
>How can I get bonded potential between beads of 3 atoms from AA
>simulation? Do I have to specify energy groups (energgrps) before the
>run in my mdp and then use g_energy?
>
>Thank you
>
>Steven
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Re: [gmx-users] Virtual sites setting

[Broadbent, Richard]

Dear Rajiv,

Without a clear explanation of what you are doing and the specific error
message from grompp it is impossible to offer any sensible advice.

Other pieces of information which might be useful would be, the topology
file, the actual grompp line, and the gro file for a single CO molecule

Richard

On 28/03/2013 20:02, "라지브간디"  wrote:

>Dear gmx,
>
>I would like to set virtual sites for CO molecules with some specific
>charge. 
>
>As per GROMACS manual, I've created virtual site2 in topology file for
>CO. Also, given the information in .rtp file as well as added the
>COM(center of mass) atom in .gro file. However, when I use gromp, it
>shows COM not found.
>
>Please need an advice. Thanks.
>
>Rajiv

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Re: [gmx-users] virtusal site setting

[Broadbent, Richard]

Dear Rajiv,

The .itp looks fine to me except for the coefficient in the virtual site
which I think should be much closer to 0.5.

If the issue is that you don't have the coordinate on the COM in your .gro
file then you will need to generate it yourself. If you have one CO
molecule which you use to build a box using say genconf I would suggest
just working out the position by hand and modifying the .gro manually. If
that is not the case (ie. you have many CO molecules at all stages of the
process) it's time to get out your favourite programming language and
write a program which reads a .gro and adds the COM to each molecule and
writes it out again.


Richard


On 29/03/2013 06:41, "라지브간디"  wrote:

>
>
>Dear Richard,
>
>
>For instance, To simulate the hemoglobin with heme ligated CO, would like
>to set the charges on center of mass of CO.
>
>
>How do i include the virtual sites atom in co-ordinates (x,y and z)?. I
>added the virtual sites line in topology as follows:
>
>[ moleculetype ]
>; molname   nrexcl
>CMO 2
>
>
>[ atoms ]
>; idat type res nr  residu name at name cg nr   charge
>1   OM  1   CMO O 1  -0.8515.9994
>2   CM  1   CMO C 1  -0.7512.0110
>3   COM1   CMO M11.60 0.000
>
>
>[ bonds ]
>; i j   funct   length  force.c.
>1   2   1  0.1128  933032.0
>
>
>[ virtual_sites2 ]
>; Vsite from  funct   a
>3   1   2   1   0.042880515
>
>
>
>
>
>
>Also, i entered in .atp and .rtp file. Could you please give some
>procedure to do this? Thanks in advance.
>
>
>
>
>Dear Rajiv, 
>
>Without a clear explanation of what you are doing and the specific error
>message from grompp it is impossible to offer any sensible advice.
>
>Other pieces of information which might be useful would be, the topology
>file, the actual grompp line, and the gro file for a single CO molecule
>
>Richard 
>
>On 28/03/2013 20:02, "��"  wrote:
>
>>Dear gmx, 
>> 
>>I would like to set virtual sites for CO molecules with some specific
>>charge. 
>> 
>>As per GROMACS manual, I've created virtual site2 in topology file for
>>CO. Also, given the information in .rtp file as well as added the
>>COM(center of mass) atom in .gro file. However, when I use gromp, it
>>shows COM not found.
>> 
>>Please need an advice. Thanks.
>> 
>>Rajiv 
>

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Re: [gmx-users] Setting virtual sites ?

[Broadbent, Richard]

Please include the full error message and the grompp line you used when
asking for help. Without them I can't tell what you are doing.

Richard

On 04/04/2013 17:40, "라지브간디"  wrote:

>
>Dear Richard,
>
>I've included the COM in my .gro and also updated the rtp, atp and
>ffnonbonded.itp files as well as the exact coefficient value.  But when I
>use gromp I get the error that COM not found in atom type database .
>
>Actually I included the COM in atomtypes.atp like
>COM  0.
>
>As it doesn't have mass value. In addition, I included in ffnonbonded.
>Itp file by setting their LJ value as 0 ( both sigma and epsilon )
>
>Please suggest how to avoid this error.
>Thanks in advance.
>
>Rajiv
>
>
>
>Dear Rajiv, 
>
>The .itp looks fine to me except for the coefficient in the virtual site
>which I think should be much closer to 0.5.
>
>If the issue is that you don't have the coordinate on the COM in your
>.gro 
>file then you will need to generate it yourself. If you have one CO
>molecule which you use to build a box usingsay genconf I would suggest
>just working out the position by hand and modifying the .gro manually. If
>that is not the case (ie. you have many CO molecules at all stages of the
>process) it's time to get out your favourite programming language and
>write a program which reads a .gro and adds the COM to each molecule and
>writes it out again.
>
>
>Richard 
>
>On 29/03/2013 06:41, "" wrote:
>>Dear Richard, 
>>For instance, To simulate the hemoglobin with heme ligated CO, would
>>like 
>>to set the charges on center of mass of CO.
>>How do i include the virtual sites atom in co-ordinates (x,y and z)?. I
>>added the virtual sites line in topology as follows:
>> 
>>[ moleculetype ] 
>>; molname nrexcl 
>>CMO 2 
>> 
>> 
>>[ atoms ] 
>>; id at type res nr residu name at name cg nr charge
>>1 OM 1 CMO O 1 -0.85 15.9994
>>2 CM 1 CMO C 1 -0.75 12.0110
>>3 COM 1 CMO M 1 1.60 0.000
>> 
>> 
>>[ bonds ] 
>>; i j funct length force.c.
>>1 2 1 0.1128 933032.0
>> 
>> 
>>[ virtual_sites2 ]
>>; Vsite from funct a
>>3 1 2 1 0.5000
>
>> 
>> 
>> 
>> 
>> 
>> 
>>Also, i entered in .atp and .rtp file. Could you please give some
>>procedure to do this? Thanks in advance.
>> 
>> 
>> 
>> 
>>Dear Rajiv, 
>> 
>>Without a clear explanation of what you are doing and the specific error
>>message from grompp it is impossible to offer any sensible advice.
>> 
>>Other pieces of information which might be useful would be, the topology
>>file, the actual grompp line, and the gro file for a single CO molecule
>> 
>>Richard 
>> 
>>On 28/03/2013 20:02, "��" wrote:
>> 
>>>Dear gmx, 
>>> 
>>>I would like to set virtual sites for CO molecules with some specific
>>>charge. 
>>> 
>>>As per GROMACS manual, I've created virtual site2 in topology file for
>>>CO. Also, given the information in .rtp file as well as added the
>>>COM(center of mass) atom in .gro file. However, when I use gromp, it
>>>shows COM not found.
>>> 
>>>Please need an advice. Thanks.
>>> 
>>>Rajiv 
>> 
>
>
>--
>

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Re: [gmx-users] mdrun -rdd and -dds flag

[Broadbent, Richard]

On 11/04/2013 11:17, "manara r. (rm16g09)"  wrote:

>Dear gmx-users,
>
>I am having a problem with a periodic molecule and the domain
>decomposition, I wish to use a high number of processors (circa 180, but
>can obviously be reduced) and therefore need to use the -rdd or -dds
>flags (I believe), how do these value effect the simulation?
This is well documented and can be easily viewed by running

mdrun -h

In general these will be set automatically and do not need to be altered.
 
>
>The box size is 11.5 x 11.5 x 45.
>
>The polymer contains charged groups every repeating unit.

Depending on how these are setup this might be where your problem lies.
Charge groups are generally be small neutral groups of atoms say CH3 and
CH2 in a polyethylene molecule or CH in benzene. If your monomer is large
and treated as 1 charge group that could cause some problems. The exact
setup depends on how they were parameterised in the forcefield. If you are
using gromacs 4.6 or 4.6.1 with the verlet-cutoff charge groups have no
effect anyway.


>
>The error I'm getting is (note this is a test run on my home machine, not
>the cluster):
>Fatal error:
>There is no domain decomposition for 4 nodes that is compatible with the
>given box and a minimum cell size of 61.7923 nm
>Change the number of nodes or mdrun option -rdd or -dds

Since that is larger than your box size it suggests something is
dramatically wrong with your setup. The two things I know of that could
potentially cause this are strange constraints in the topology combined
with LINCS, or inappropriate choice of charge groups in the topology. My
guess is the latter.

>
>Regards
>
>Rich Manara
>PhD Student
>Chemistry
>Southampton University
>UK
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Re: [gmx-users] switching and shifting in GMX 4.6 on GPUs

[Broadbent, Richard]

On 12/04/2013 21:50, "Jesper Sørensen"  wrote:

>Hi Berk and others,
>
>Sorry it has been a long time since this issue was posted, but I got
>side-tracked from this issue with other projects. And I want to make sure
>I understand this correctly before venturing into more simulations. So
>this gets a little long winded, but I hope you will help me figure this
>out.
>
>So following up on the last emails perhaps the nomenclature is not
>consistent among the programs - which I shoudn't expect it to be either,
>so that is okay.
>I know this is the GMX list, but for clarity I will just describe what
>NAMD does, because it relates to how to run lipids in GMX (particularly
>with the GPU).
>NAMD:
>* When the switching function is on: "a smooth switching function will be
>used to truncate the van der Waals potential energy smoothly at the
>cutoff distance". 
>* A new "vdwForceSwitching" method is available as of version 2.7 - which
>applies a force-based switching function to the VDW term - similar I
>guess to how CHARMM does it.
>GMX:
>* The switch nomenclature is similar/identical to that in NAMD, in that
>the potential "energy" is switched off.

I can't speak for what NAMD does but this is not what it means in gromacs
(or any other MD code I've used). Switched adds a function (which starts
at the rcoulomb-switch/rvdw-switch) that smoothly takes both the Energy
and the Force to 0 at the cut-off radius. It is the cut-off scheme used to
parameterise the force-field I use OPLS-AA and I am certain it was used
for many others. It is not supported by the Verlet-cut-off scheme

>* The "shift" method in Gromacs is equivalent to the  "vdwForceSwitching"
>method in NAMD.

I doubt it but again I've not used NAMD, shift applies a shift to the
Non-bonded potential over its such that the Energy but not the Force goes
to 0 at the cut-off, this method does work with the Verlet cut-off scheme
and is supported on GPU's. If it is not the method used to parameterise
your forcefield, you will have to either perform simulations to check the
effect this has on your system and alter your cut-off's accordingly, or
find a paper that has done this for you in the literature.

>
>And from what Berk was saying earlier and I heard this from Prof. Lindahl
>during the GPU webinar the other day too, the "shift" method is the only
>appropriate option and switching should not be used. It seems that this
>option is the one used for lipids in NAMD and CHARMM also, so that is
>great.
>
>Now regarding the GPU's you have to run with Verlet groups and here is
>where it get confusing because looking at the comparison table on the
>website "http://www.gromacs.org/Documentation/Cut-off_schemes"; ( I've
>extracted the important features of this table below).
>The switched interactions are not available using the Verlet groups and
>that is okay since that shouldn't be used anyways. But, the shifted
>interactions are "available", but only for the "energy" - now did we not
>just agree that when it is the energy that it should be called a
>"switched interaction"? Am I missing something here?

This is an issue due to you miss understanding the places where these
terms are documented very clearly.

>
>Non-bonded interaction feature group   Verlet
>exact cut-off  shift/switch
>X
>cut-offX   
>X
>shifted interactions   force+energyenergy
>switched interactions  X   
>
>When I asked Prof. Lindahl during the excellent GPU webinar the other
>day, he said that switching was implemented and that is sort of what this
>table says too, but when we try to run a simulation using either switch
>or shift on the GPU we get the following error:
>"With Verlet lists only cut-off LJ interactions are supported"
>
>Now I can switch to an exact cut-off method at the cost of making the
>potential abruptly change to zero at the cut-off - minimizing the
>abruptness can be achieved by extending the cut-off, but then for the
>lipids CHARMM, MARTINI, and others, the cut-off seems to be an integral
>part of the force field development and changing it could prove
>problematic. So this leaves me to think that lipids simulations shouldn't
>be run on the GPU as it is currently, at least not without extensive
>testing.

In the 4.6 manual and in the online documentation it explains about new
options which are used to control the cut-off scheme see:
http://manual.gromacs.org/online/mdp_opt.html#el

Using these you can use a shifted cut-off and if necessary for your
Force-field correct for the mild discontinuity in the force either by
looking in the literature or as Berk Hess described below combined with
some test simulations.

I hope this helps clarify things,

Richard

>
>I'd appreciate any comments to all this rambling that can help clarify
>this for me...
>
>Thanks,
>Jesper
>
>
>
>
>
>On Ja

Re: [gmx-users] Issue running gromacs in Cluster

[Broadbent, Richard]

On 13/05/2013 08:46, "Sainitin Donakonda"  wrote:

>Hello,
>
>I am trying to run 20 ns protein ligand simulation on cluster using
>following MD.MDP file
>
>; 7.3.3 Run Control
>integrator  = md; leap-frog integrator
>dt  = 0.002 ; 2 fs
>nsteps  = 500; maximum number of steps
>to integrate
>
>
>
>; 7.3.8 Output Control
>nstxout = 200 ; suppress .trr output
>nstvout = 200; suppress .trr output

This writes out every 0.4 ps I doubt that¹s what you want

>nstenergy   = 1000  ; save energies every 2 ps
>nstlog  = 1000  ; update log file every 2 ps
>nstxtcout   = 1000  ; write .xtc trajectory every 2 ps
>energygrps  = Protein LIG
>
>; 7.3.9 Neighbor Searching
>nstlist = 5 ; [steps] freq to update neighbor
>list
>ns_type = grid  ; method of updating neighbor list
>pbc = xyz   ; periodic boundary conditions in
>all directions
>rlist   = 1.2   ; [nm] cut-off distance for the
>short-range neighbor list
>
>; 7.3.10 Electrostatics
>coulombtype = PME   ; Particle-Mesh Ewald
>electrostatics
>rcoulomb= 1.2   ; [nm] distance for Coulomb
>cut-off
>
>; 7.3.11 VdW
>vdwtype = switch   ; twin-range cut-off with rlist
>where rvdw >= rlist
>rvdw= 1.2   ; [nm] distance for LJ cut-off
>rvdw_switch = 0.8   ; Start switching th LJ potential
>DispCorr= EnerPres ; apply long range dispersion
>corrections for energy
>
>; 7.3.13 Ewald
>fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
>when using PME
>pme_order   = 4 ; interpolation order for PME, 4 =
>cubic
>ewald_rtol  = 1e-5  ; relative strength of
>Ewald-shifted potential at rcoulomb
>
>; 7.3.14 Temperature Coupling
>tcoupl  = V-rescale ; temperature
>coupling with Berendsen-thermostat
>tc_grps = Protein_LIG Water_and_ions; groups to couple
>seperately to temperature bath
>tau_t   = 0.10.1; [ps] time
>constant for coupling
>ref_t   = 300300; [K] reference
>temperature for coupling
>
>; Pressure coupling
>pcoupl  = Parrinello-Rahman ; pressure coupling is on for
>NPT
>pcoupltype  = isotropic ; uniform scaling of box
>vectors
>tau_p   = 2.0   ; time constant, in ps
>ref_p   = 1.0   ; reference pressure, in bar
>compressibility = 4.5e-5; isothermal compressibility
>of
>water, bar^-1
>refcoord_scaling= com
>
>; 7.3.17 Velocity Generation
>gen_vel = no; velocity generation turned off
>
>; 7.3.18 Bonds
>constraints = all-bonds ; convert all bonds to constraints
>constraint_algorithm= LINCS ; LINear Constraint Solver
>continuation= yes   ; apply constraints to the start
>configuration
>lincs_order = 4 ; highest order in the expansion
>of
>the contraint coupling matrix
>lincs_iter  = 1 ; number of iterations to correct
>for rotational lengthening
>lincs_warnangle = 30; [degrees] maximum angle that a
>bond can rotate before LINCS will complain
>
>
>*and im using following commands dividing 20 ns to 10 ns each via
>extending
>simulation*
>
>
>*#This is the first simulation MD.mdp file contains 20 ns setup*
>grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
>MD_first10.tpr
>
>mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16
>
>*#This extends 10 ns simulation*
>tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr
>
>mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
>MD_first10.cpt -append -np 16
>
>
>But it is crashed giving following error
>
>*XTC error - maybe you are out of quota?*
>*
>*
>*dont know why it happened it is because as im saving .trr file every
>200ps? is it creating large files? or should i give different name in
>extending simulation?*

No you are writing every 200 steps not ps this is explained in the
turtorials and the manual
You can check the file size by looking at ls -lh my guess is both the trr
and xtc will be gigantic

>*
>*
>*Please help*
>*
>*
>*Thanks,*
>*Nitin*
>-- 
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Re: Aw: Re: [gmx-users] GPU-based workstation

[Broadbent, Richard]

I've been running on my Universities GPU nodes these are one E5-xeon (6-cores 
12 threads)  and have 4 Nvidia 690gtx's. My system is 93 000 atoms of DMF under 
NVE.  The performance has been a little disappointing ~10ns/day. On my home 
system using a core i5-2500 and a nvidia 560ti I get 5.4ns/day for the same 
system. On our HPC system using 32 nodes each with 2 quad-core xeon processors 
I get 30-40ns/day.

I think that to achieve reasonable performance the system has to be balanced 
between CPU's and GPU's probably getting 2 high end GPU's and a top end xeon E5 
or core i7 would be a good choice.


Richard

From: lloyd riggs mailto:lloyd.ri...@gmx.ch>>
Reply-To: Discussion users mailto:gmx-users@gromacs.org>>
Date: Saturday, 25 May 2013 12:02
To: Discussion users mailto:gmx-users@gromacs.org>>
Subject: Aw: Re: [gmx-users] GPU-based workstation

More RAM the better, and the best I have seen is 4 GPU work station.  I can 
use/have used 4.  The GPU takes 2 slots though, so a 7-8 PCIe board is really 
3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 slot 
board really holds 8 or 10 GPU's).  There's cooling problems though with GPU's, 
as on a board there packed, so extra cooling things may help not blow a GPU, 
but I would look for good ones (ask around), as its a video game market and 
they go for looks even though its in casing?  The external RAM (not onboard GPU 
RAM) helps if you do a larger sim, but I dont know performance wise, the 
onboard GPU, the more RAM the marrier...so yes, normal work stations you can 
get 4 GPU's for a 300 US$ board, but then the price goes way up (3-4000 US$ for 
an 8-10 gpu board).  RAM ordered abroad is also cheep, 8 or 16 MB Vs. Shop...I 
have used 4 GPU's but only on tests software, not Gromacs, so would be nice to 
see performance...for a small 100 atom molecule and 500 solvent, using just the 
CPU I get it to run 5-10 minutes real  for 1 ns sim, but tried simple large 800 
amino, 25,000 solvent eq (NVT or NPT) runs and they clock at around 1 hour real 
for say 50 ps eq's

Stephan

Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
Von: "James Starlight" mailto:jmsstarli...@gmail.com>>
An: "Discussion list for GROMACS users" 
mailto:gmx-users@gromacs.org>>
Betreff: Re: [gmx-users] GPU-based workstation
Dear Dr. Watkins!

Thank you for the suggestions!

In the local shops I've found only Core i7 with 6 cores (like Core
i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
than with 4 cores in case of i7 cpu (assuming that I run simulation in
cpu+gpu mode )?

Also you've mentioned about 4 PCeI MD. Does it means that modern
work-station could have 4 GPU's in one home-like desktop ? According to my
current task I suppose that 2 GPU's would be suitable for my simulations
(assuming that I use typical ASUS MB and 650 Watt power unit). Have
someone tried to use several GPU's on one workstation ? What attributes of
MB should be taken into account for best performance on such multi-gpu
station ?

James

2013/5/25 lloyd riggs mailto:lloyd.ri...@gmx.ch>>

> There's also these, but 1 chip runs 6K US, they can get performance up to
> 2.3 teraflops per chip though double percission...but have no clue about
> integration with GPU's...Intell also sells their chips on PCIe cards...but
> get only about 350 Gflops, and run 1K US$.
>
> http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
> http://www.xilinx.com/
>
> They can design them though to fit a PCIe slot and run about the same, but
> still need the board, ram etc...
>
> Mostly just to dream about, they say you can order them with radiation
> shielding as well...so...
>
> Stephan Watkins
>
> *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
> *Von:* "James Starlight" 
> mailto:jmsstarli...@gmail.com>>
> *An:* "Discussion list for GROMACS users" 
> mailto:gmx-users@gromacs.org>>
> *Betreff:* [gmx-users] GPU-based workstation
> Dear Gromacs Users!
>
>
> I'd like to build new workstation for performing simulation on GPU with
> Gromacs 4.6 native cuda support.
> Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
> and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
> with SD integrator)
>
>
> Now I'd like to build multi-gpu wokstation.
>
> My question - How much GPU would give me best performance on the typical
> home-like workstation. What algorithm of Ncidia GPU integration should I
> use (e.g SLI etc) ?
>
>
> Thanks for help,
>
>
> James
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Re: [gmx-users] OPLSAA.ff

[Broadbent, Richard]

The conversion is in ffnonbonded.itp. However, unless you plan to modify
the forcefield you shouldn't need this.

Richard

On 01/06/2013 00:57, "Hari Pandey"  wrote:

>Dear Gromacs users,
>
>I am a new user and I have some questions
> I confused about indexing.  in atomtypes.atp  clearly  we can know the
>index is for what kind of atom but  in ffbondedtype.itp there is
>different kind of the indexing  so I confused how do i pathch the force
>field . 
>Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen
>bonded to oxygen)
>but definitively I dont know what type of bond makes the carbon atoms like
>C_2, C_3 or C *
>Can somebody help me what represents in ffbonded.atp.
>for example : opls_083  means S in RSR , opls_091  means CH2 in RCH2SR
>but what type of atoms are C*, C_2, C_3 ,  CT, CM, CS, LP, CT_2, CT_3,
>CW, NB etc.  
>
>
>could you please provide me idea or list for that if somebody have.
>Thanks
>
>
>In Oplsaa.ff the indexing is  as follows :
>
>atomtypes.atp
>
>
>opls_0791.00800  ; H(O) ALCOHOLS JPC,90,1276 (1986)
> opls_080   15.03500  ; CH3 IN METHANOL   JPC,90,1276 (1986)
> opls_081   14.02700  ; CH2 IN ETHANOLJPC,90,1276 (1986)
> opls_082   32.06000  ; S   IN H2SJPC,90,6379 (1986)
> opls_083   32.06000  ; S   IN RSHJPC,90,6379 (1986)
> opls_084   32.06000  ; S   IN RSRJPC,90,6379 (1986)
> opls_085   32.06000  ; S   IN RSSR   JPC,90,6379 (1986)
> opls_0861.00800  ; H   IN H2SJPC,90,6379 (1986)
> opls_0871.00800  ; H(S) IN RSH   JPC,90,6379 (1986)
> opls_088   15.03500  ; CH3 IN CH3SH  JPC,90,6379 (1986)
> opls_089   14.02700  ; CH2 IN CH3CH2SH   JPC,90,6379 (1986)
> opls_090   15.03500  ; CH3 IN CH3SR  JPC,90,6379 (1986)
> opls_091   14.02700  ; CH2 IN RCH2SR JPC,90,6379 (1986
>
>The ffbonded.itp is as follows ; Some esoteric OPLS atomtypes are not
>freely available (or depreciated).
>; Interaction types involving these have been commented out. [ bondtypes ]
>; ij  func   b0  kb OWHW  10.09572   502080.0
>  ; For TIP4F Water - wlj 1/98 OWLP  10.01750   753120.0   ;
>-idem- C*HC  10.10800   284512.0   ; C C3  1
>  0.15220   265265.6   ; END C_2   C3  10.15220   265265.6   ;
>END C_3   C3  10.15220   265265.6   ; END C CA  1
>0.14900   334720.0   ; wlj 8/97 C_2   CA  10.14900   334720.0   ;
>wlj 8/97 C_3   CA  10.14900   334720.0   ; wlj 8/97 C CB
>10.14190   374049.6   ; GUA C_2   CB  10.14190   374049.6   ;
>GUA C_3   CB  10.14190   374049.6   ; GUA C CM  1
>0.14440   343088.0   ; THY C_2   CM  10.14440   343088.0   ; THY
>C_3   CM  10.14440   343088.0   ; THY C CS  10.14900
> 334720.0   ; C_2   CS  10.14900   334720.0   ; C_3   CS  1
> 0.14900   334720.0   ; C CT  10.15220   265265.6   ; C_2
>CT  10.15220
> 265265.6   ; C_3   CT  10.15220   265265.6   ; C CT_21
> 0.15220   265265.6   ; AA Calpha C_3   CT_210.15220   265265.6
>; AA C-term NOON  10.12250   460240.0   ; wlj nitro CSCW
>10.13670   456892.8   ; wj/nm CSCS  10.14240
>392459.2   ; -idem- CSCB  10.14240   392459.2   ; -idem- CS
> HA  10.10800   307105.6   ; -idem- CUNB  10.13200
>343088.0   ; -idem- CUCA  10.14210   392459.2   ; -idem- CU
> HA  10.10800   307105.6   ; -idem- NANB  10.13490
>334720.0   ; -idem- OSNB  10.13990   386601.6   ; -idem- OS
> CR  10.13570   386601.6   ; -idem- C3C3  10.15260
>217568.0   ; Ethane C!C!  10.14600   322168.0   ; wlj C!
>CS  10.14600   322168.0   ; wlj
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Re: [gmx-users] vsite as interaction site for COM of benzene

[Broadbent, Richard]

Dear Thomas,

Whilst in principle a constraint should do what you are asking, you might be
better off using multiple vsites to solve the problem so that there is an
algebraic as apposed to numerical mapping of the forces. My immediate
thought is to use two type 3 (or if necessary type 3fd) virtual sites to
define two points near the centre of the benzene. You could then place your
tabulated potential on a type 2 virtual site between these two. I believe
that should algebraically link all the atomic sites together making the
process more stable and it should be quite easy to transfer it to other
systems.

On a separate note why if you are coarse graining the benzenes to a single
point particle are you then maintaining all the atoms? Could you go a stage
further and map the atoms onto 3 non interacting point masses? That would
maintain angular momentum etc. whilst reducing the computational overhead.
Although it becomes very complex to implement if your benzene's are in the
backbone of a polymer.

Hope that helps,

Richard

On 08/06/2012 18:18, "Thomas Schlesier"  wrote:

> Hi all,
> 
> i have a more conceptional question, for using vsites as
> interaction-centers for coarse-grained particles:
> 
> First the simple case:
> I want to simulate one benzene molecule (atomistic - aa) in
> coarse-grained (cg-) benzene (each benzene molecule as a single
> particle). For the cg-cg interaction of the benzene i have calculated a
> table potential.
> 
> But for the aa-cg interaction I'm a little bit clueless:
> I want to use the COM of the aa-benzene as an interaction-site. But
> there is no vsite, which i could construct from 6 atoms.
> Side-note: The vsite would not interact with the with the atoms, only
> with cg-benzenes
> 
> So there are two ideas:
> 
> 1) Using one '3out'-vsite, which is construted from 3 non-neighbour
> atoms (if we had mesitylene instead of benzene, it would be the three
> C-atoms to which only hydrogens are bound). The the force from the aa-cg
> interaction would be distributed to these three atoms and i would hope
> that the bond-constraints would do 'the rest' (i.e. they would mimick
> that the whole aa-benzene molecule interacts with the cg-particles)
> 
> 2) Using two '3out'-vsites. First viste the same as in (1), the second
> comes from the set of the other three C-atoms. These two vsites, should
> be at the same position (more or less, for a perfect energy-minimized
> benzene molecule it would be so; but i would assume the error is only
> minimal). Since the potential is pair-additive, i would use for this
> table potential only half of the potential, so that the potential of
> both particles would add up to the 'true' potential. The forces would be
> calculated from the 'half-potential'.
> 
> Big questions is now:
> Are (1) and (2) equivalent?
> (2) Seems like the 'right way' to do.
> But (1) would be easier to implement :) But the big question is, if the
> bond-constraints would correct the approximation, that only 3 out of 6
> atoms have a direct interaction with the cg-particles.
> 
> Side note:
> The real system is a little more complex. There are fracments of
> molecules where i could not really construct two vsites which would have
> more or less the same position. In this case, method (1) would really help.
> 
> Any ideas?
> Greetings
> Thomas

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Re: [gmx-users] angle constraints

[Broadbent, Richard]

An Angle constraint amounts to fixing a triangle. To do this you need to
constrain the distances between all the atoms as you know the of the bonds
6064, 6063 and 6063, 6065 and the angle between the two bonds it is a
trivial geometry problem calculate the length of the third side of the
triangle (6064,6065). However, as you are attempting to hold these atoms in
a straight line I would suggest that a type 2 virtual site might (depending
on your system) be a better idea.

Richard


On 24/07/2012 07:21, "tarak karmakar"  wrote:

> Oh ! Thnaks
> I saw that table, the angle_restrain option is there but not constraints .
> Anyway if suppose, I fix the distance between the two terminal atoms
> of the molecule, the angle will eventually be fixed at a particular
> given value. Is that the logic ?
> Actually I searched for this problem so many times but didn't get
> proper clue; in one of those mails I saw someone has dealt with some
> dummy atoms. I could not able to digest that logic.
> 
> On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham 
> wrote:
>> On 24/07/2012 3:21 PM, tarak karmakar wrote:
>>> 
>>> Dear All,
>>> 
>>> 
>>> I am constraining one angle in my protein sample by incorporating " [
>>> constraints ]" block in topology file as
>>> 
>>> 
>>> [ constraints ]
>>> ;  index1  index2  index3   funct angle
>>>   6064 6063 6065 1   180.0
>>> 
>>> while doing that its showing the following error
>>> 
>>> Program grompp, VERSION 4.5.5
>>> Source code file: topdirs.c, line: 174
>>> 
>>> Fatal error:
>>> Invalid constraints type 6065
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>> 
>> 
>> As you will see in table 5.6, this is not a valid option for [constraints] -
>> you can only specify bonds. You will need to construct a triangle of bond
>> constraints.
>> 
>> Mark
>> 
>> 
>>> 
>>> 
>>> Then I rechecked the angle block, that specific angle is there in that
>>> angle section, part of it as follows
>>>   6039  6057  6058 1
>>>   6039  6057  6059 1
>>>   6058  6057  6059 1
>>>   6064  6063  6065 1
>>>   6067  6066  6068 1
>>>   6067  6066  6069 1
>>>   6068  6066  6069 1
>>>   6071  6070  6072 1
>>>   6071  6070  6073 1
>>>   6072  6070  6073 1
>>> 
>>> [ constraints ]
>>> ;  index1  index2  index3   funct angle
>>>   6064 6063 6065 1   180.0
>>> 
>>> [ dihedrals ]
>>> ;  aiajakal functc0c1
>>> c2c3c4
>>> 
>>> 
>> 
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> 

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Re: [gmx-users] angle constraints

[Broadbent, Richard]

Virtual sites are by definition have no mass.

If you simply ignore the mass of the carbon the molecule will be too light
and its translational momentum will therefore be too small meaning it will
move too quickly.

If you place half the mass of the carbon on each oxygen the moment of
inertia will be wrong and the molecule will spin too slowly.

In practice you have to decide what you want to loose or if a balance
between the two is better.

Richard


On 25/07/2012 14:44, "Thomas Schlesier"  wrote:

> Ok, read the topic about the acetonitril. But i'm somewhat clueless:
> 
> Why is the following setup wrong:
> Use 2 particles as normal atoms. Put the third as a dummy in between.
> Give each particle its 'normal' mass?
> I would assume that this system should have the right mass and moment of
> inertia, due to the fact the all individual masses and the positions one
> the particles would be correct.
> 
> Only idea i have, why this setup could be flawed, would be that the
> third particle does only interact indirectly through the other two
> particles (i mean, virtual site interacts normally with all othe
> particles, but the force which would act on the dummy get redistributed
> to the other particles)... and then it's mass does not come into play,
> since it new position is determined only by the other two particles. so
> the complete molecule would move with a reduced mass?!?
> 
> Can anyone comment on this?
> 
> greetings
> thomas
> 
> 
> On 25/07/2012 10:08 PM, Thomas Schlesier wrote:
>> What you have done there looks very strange...
>> easiest wy would be:
>> define the two oxygens as normal atoms (1,2), give them a bondlength
>> twotimes the C-O bond length
>> define the carbon as a dummy (3), while you construct it's position
>> from both oxygens with a=0.5
>> one thing i don't know is how to handle the mass:
>> 1) give both oxygen half of the system mass
>> 2) give all atoms their normal mass
>> would tend to (2)
> 
> One should want to get both the total mass and the moment of inertia
> correct...
> http://lists.gromacs.org/pipermail/gmx-users/2003-September/007095.html.
> 
> Mark
> 
>> 
>> greetings
>> thomas
>> 
>> Am 25.07.2012 13:15, schrieb gmx-users-request at gromacs.org:
>>> How to choose the positions of the dummy atoms while constraining the
>>> angle for a linear triatomic molecule?
>>> The topology for a such molecule ( af for example CO2 ) is as follows
>>> 
>>> [ moleculetype ]
>>> ; Namenrexcl
>>> CO2  2
>>> 
>>> [ atoms ]
>>> ;   nr   type  resnr residue  atom   cgnr charge mass
>>> typeBchargeB  massB
>>> ; residue 503 CO  rtp CO   q  0.0
>>>   1 D1503 CO D1  1  0 21.90158
>>>; qtot 0
>>>   2 D2503 CO D2  2  0 21.90158
>>>; qtot 0
>>>   3 CE503 CO CO  30.7 0.0
>>>; qtot 0.7
>>>   4 OE503 COOC1  4  -0.35 0.0
>>>; qtot 0.35
>>>   5 OE503 COOC2  5  -0.35 0.0
>>>; qtot 0.35
>>> [ constraints ]
>>> ;  ai  aj funct   b0
>>> 1 2 1   0.2000
>>> 
>>> [ dummies2 ]
>>> ;  aiajak   funct   a
>>>  3 1 2   1   0.0170
>>>  4 1 2   1   0.1000
>>>  5 1 2   1   0.2170
>>> 
>>> 
>>> [ exclusions ]
>>> 3 4 5
>>> 4 5 3
>>> 5 4 3
>>> 
>>> 
>>> 
>>> The .rtp file for CO2
>>> 
>>> [ CO ]
>>>   [ atoms ]
>>>  D1 D1  0.   1
>>>  D2 D2  0.   2
>>>  COCE  0.70003
>>>  OC1  OE -0.3500   4
>>>  OC2  OE -0.35005
>>>   [ bonds ]
>>>  CO  OC1
>>>  CO  OC2
>>> 
>>> 
>>> Can anyone please check above file parts whether I'm doing correct or
>>> not ?
>> 

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Re: [gmx-users] trajectory file formats

[Broadbent, Richard]

As these are binary files the formatting can be quite complex I would
suggest using the library available here:

http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library

This includes all the functions necessary to read/write these formats and is
licensed under LGPL.

Richard


On 13/08/2012 14:48, "Jim Kress"  wrote:

> I have written a unique MD program and want to output a full-precision
> trajectory containing coordinate, velocity, and force information in a .trr
> or a .trj formatted file. 
> 
> Where in the gromacs code can I find a description of the formats of these
> files and an example of how they are written?
> 
> Alternately, I can write .gro files and append the force information in the
> same format as the velocity information.  Will the gromacs utilities ignore
> the extra information in the generated .gro files or will it cause them to
> fail?
> 
> Any advice/ suggestions would be appreciated.
> 
> Thanks.
> 
> Jim
> 
> 

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Re: [gmx-users] Holes in the solvent!

[Broadbent, Richard]

Dear Arman,

I've noticed a similar effect where large voids appear in a solvent when
running long nose-hoover NVT simulations. I have checked and it is not a pbc
artefact.
I found that if I turn the thermostat off the holes go away. I've also found
that reducing the number of cores removes the holes. I am currently
investigating this for a bug report I submitted (
http://redmine.gromacs.org/issues/1012 )

It would be helpful if you could let me know if your using a nose-hoover
thermostat and if so have a look at what happens if you run the system on
fewer cores, and what happens if you turn off the thermostat (and run nve)
after the system has equilibrated.

Thanks,

Richard



On 30/10/2012 05:46, "Arman Mahboubi Soufiani" 
wrote:

> Dear Chris,
> 
> Thank you for your directions. NaCl concentration in my system is 0.14 M
> and I often visualize the whole system and can see the ions around the
> system but not in crystal form!
> Well, it sounds really strange to me! And I don't know if I proceed with
> such a system, I get scientific results or not?!
> I appreciate your further helps.
> 
> Best Regards
> 
> Arman
> 
> On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale <
> chris.ne...@mail.utoronto.ca> wrote:
> 
>> In addition to the comments of Dallas Warren, which seems quite possible
>> and should be checked,
>> are you sure that you are seeing real holes and not just salt crystals
>> that look like holes when you render only
>> the waters with VMD? I have found that, at NaCL concentrations above 1 M,
>> lipid bilayers catalyze the formation
>> of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field
>> for ions. These crystals looked a lot
>> like vacuum holes to me until I visualized the salt.
>> 
>> Chris.
>> 
>> -- original message --
>> 
>> I am simulating a protein on a polymer surface for further adsorption free
>> energy calculation.
>> However, after performing the NVT run either for short or long durations I
>> found out that couple of holes appear in the physiological saline solution
>> (solvent)!!!
>> Additionally, even proceeding with a long NPT run the holes are still
>> present in the system.
>> I would be thankful if you could direct me what could be source of such a
>> strange outcome.
>> 
>> Best Wishes
>> 
>> Arman
>> 
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[gmx-users] Virtual Sites in a polymer backbone

[Broadbent, Richard]

I wish to keep certain parts of the backbone of my polymer rigid and planar,
as my primary interest is in the long length and timescale motion of the
polymer. 

I am attempting to utilise virtual sites as a means to keep aromatic groups
rigid and planar. My intention is to replace groups such as phenyl rings and
connected 5 and 6 member rings (similar to Phthalimide) with 3 reference
sites, then virtualise all the atomic sites. I'm going to use standard type
3 virtual sites and planned on constraining the relative positions of the 3
reference points. 

My plan is to pick sites such that the 3 eigenvalues of the moment of
inertia tensor, the centre of mass, and the total mass of the system are
conserved. As the system is two dimensional this amounts to a total of 6
non-linear equations for 9 variables which requires either additional
constraints or a physically motivated guess to solve.

I've searched the mailing list but have been unable to find any previous
attempts at this. I was wondering if anyone knew of a reference where this
had been attempted or if there had been any previous discussions about an
approach similar to this?

I am also very open to alternative approaches to holding these groups
planar.

Many thanks,

Richard

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Re: [gmx-users] Virtual Sites in a polymer backbone

[Broadbent, Richard]

> 
> Any particular reason why improper dihedrals would not be suitable?  They are
> significantly easier to implement.
Yes the force field parameters for the molecule are not known and I am
therefore fitting the parameters to Density Functional Theory. If I allow
the units to move out of plane even slightly their will be additional
parameters to fit which will make the problem unfeasibly computationally
expensive.

Thank you for the suggestion,

Richard

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Re: [gmx-users] how to calculate the normal of plane for Tryptophan or how to get the comparison matrix in g_rms

[Broadbent, Richard]

Have you thought about using the cross product. If you took the cross product 
of the unit vector in the direction of every atom starting from atom 1 then 
moved on to starting from atom 2 and so on you would have a set of vectors 
normal to every group of three atoms. If you then normalised them and defined 
one to be pointing upwards you could then ensure using dot products that they 
all pointed the same way, a condition like if a.b <0 b=-b would probably work 
you could then take the mean of the vectors. This should give an average normal 
vector to the plane of the molecule.

If you’re going to be doing this a lot I would suggest removing the inherent 
double counting (r12=-r21).

You could also think about weighting normal vectors in the averaging, for 
instance you could do it based on the sine of the angle between the vectors 
which generated them, or the mass of the atoms (H’s will more out of plane than 
carbons typically)

Hope that’s helpful

Richard

On 15/10/2011 15:45, "xiaodong huang"  wrote:

I send this message yesterday, but I myself donot see this message, so, I send 
it again, very sorry for the spam.
Dear gmxer's
I am simulating a protein, want to calculate the normal of plane for Tryptophan 
residue amino acid in that protein.
We need to take into account that, in simulation, atoms of TRP vibrate all the 
time, and they are not always on the same plane:
If they were on the same plane in my simulation, to calculate the normal would 
be rather straighforward.
As those atoms are not on the same plane, I think my calculation should be 
something like least square fitting. I look at g_rms command,
and plan to calculate the normal in following steps:
1. create a Tryptophan with ideal configuration, where all 8 C atom and N atom 
(except CB atom) should be in the same plane,
I put these 9 atoms in xy plane, and the normal of this TRP molecule is 
just z axis
2.I then calculate the rms between the TRP residue in my simulation and that 
ideal TRP molecule
3.If I know the rotate matrix (e.g. how to rotate the TRP in my simulation in 
the least-squares fitting of rms calculation), then I
   just rotate z axis (0,0,1) back ( in other words, multiple z axis (0,0,1) 
with the inverse of that rotate matrix) to get the plane normal
   for TRP in my simulation.
So, I am wondering how to know the the rotate matrix when g_rms do the 
least-squares fitting? Is that in the comparison matrix
dumped by the -bin option? If so, how to read the rotate matrix from that 
binary file produced by -bin option?
Or, if there is other way that I can calculate plane normal for TRP?
Thank you so much for your kind help.
yours
xiaodong
school of chem, ANU



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Re: [gmx-users] output logfile

[Broadbent, Richard]

Hi Sanku

The ^M ‘s in that sample indicate a line break that was issued by a different 
text formatting standard. This frequently happens if files are generated in one 
OS say Windows then viewed in another say unix. Is your version of gromacs 
compiled for your system or was is compiled for a different machine/OS?

Richard


On 03/12/2011 19:50, "Sanku M"  wrote:

Hi,
 It might be a very minor issue but I find in versions of gromacs 4.5.4, the 
output log file ( in verbose mode) writes the progress of the simulation in a 
single line ( unlike in previous gromacs 4.0.7 version) where it used to write 
the progress in a new lines. As a result, in gromacs4.5.4, opening a logfile or 
issuing unix 'tail' command to see last few lines becomes a bit time-consuming 
as the progress is written in a single line.

An example is shown below for gromacs 4.5.4:
  ^Mstep 2100, will finish Sat Dec  3 19:55:12 2011vol 0.79  imb F  0% ^Mstep 
2200, will finish Sat Dec  3 19:54:59 2011vol 0.80  imb F  1% ^Mstep 2300, will 
finish Sat Dec  3 19:54:49 2011vol 0.79  imb F  1% ^Mstep 2400, will finish Sat 
Dec  3 19:54:40 2011vol 0.80  imb F  0% ^Mstep 2500, will finish Sat Dec  3 
19:54:31 2011vol 0.80  imb F  1% ^Mstep 2600, will finish Sat Dec  3 19:54:22 
2011vol 0.80  imb F  1% ^Mstep 2700, will finish Sat Dec  3

I wonder whether there is an fix for this minor issue.

Thanks
Sanku




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Re: [gmx-users] Settles vs. 3 normal constraints (energy conservation problem)

[Broadbent, Richard]

For my system reducing shake-tol greatly improves the energy conservation
generally 1.0e-7 is the largest I would use. However if you want very good
energy conservation 1.0e-9 or lower might be needed.

This effect might only be for my system but I think it might help here too

Richard

On 25/06/2013 08:45, "Mark Abraham"  wrote:

>On Tue, Jun 25, 2013 at 1:34 AM, S. Alireza Bagherzadeh
> wrote:
>> Dear All,
>>
>> I have a box of 3073 tip4p water molecules. I do a 250ps nvt, then 250
>>ps
>> npt and finally a 1 ns nve (production run).
>>
>> I used the opls forcefield and I copied the tip4p.itp to my working
>> directory (in order to be able to make changes).
>>
>> In one case I used the [ settles ] directive to constraint water
>>molecules.
>> .top file:
>>
>> ; Topology for 3087 TIPT4P waters
>>
>> #include
>> 
>>"/global/software/gromacs/gromacs-4.5.5/share/gromacs/top/oplsaa.ff/force
>>field.itp"
>> ;SOL
>> ;---
>> ; water topology - liquid phase
>> #include "./tip4p.itp"
>> ;
>> [ system ]
>> ; Name
>> A box of 216 tip4p for protocol testing
>>
>> [ molecules ]
>> ; Compound   #mols
>> SOL  3073
>>
>>
>> .itp file:
>> ; Note the strange order of atoms to make it faster in gromacs.
>> ;
>> [ moleculetype ]
>> ; molname   nrexcl
>> SOL 2
>>
>> [ atoms ]
>> ; idat type res nr  residu name at name cg nr   charge
>> 1   opls_1131   SOL  OW 1   0.0
>> 2   opls_1141   SOL HW1 1   0.52
>> 3   opls_1141   SOL HW2 1   0.52
>> 4   opls_1151   SOL  MW 1  -1.04
>>
>> #ifndef FLEXIBLE
>> [ settles ]
>> ; OWfunct   dohdhh
>> 1   1   0.095720.15139
>> #else
>> [ bonds ]
>> ; i j   funct   length  force.c.
>> 1   2   1   0.09572 502416.0 0.09572502416.0
>> 1   3   1   0.09572 502416.0 0.09572502416.0
>>
>> [ angles ]
>> ; i j   k   funct   angle   force.c.
>> 2   1   3   1   104.52  628.02  104.52  628.02
>> #endif
>>
>> [ exclusions ]
>> 1   2   3   4
>> 2   1   3   4
>> 3   1   2   4
>> 4   1   2   3
>>
>> ; The position of the virtual site is computed as follows:
>> ;
>> ;   O
>> ;
>> ;   D
>> ;
>> ;   H   H
>> ;
>> ; const = distance (OD) / [ cos (angle(DOH))* distance (OH) ]
>> ; 0.015 nm  / [ cos (52.26 deg) * 0.09572 nm]
>>
>> ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
>>
>> [ virtual_sites3 ]
>> ; Vsite fromfunct   a   b
>> 4   1   2   3   1   0.128012065 0.128012065
>>
>> .mdp file:
>> 
>>;
>>-;
>> 
>>;
>>-;
>> ; Run control
>> integrator   = md   ; Leap-frog algorithm
>> tinit= 0; starting time [ps]
>> dt   = 0.001; time step [ps]
>> nsteps   = 25   ; number of steps
>> nstcomm  = 100  ; frequency for center of mass
>>motion
>> removal [steps]
>> 
>>;
>>-;
>> 
>>;
>>-;
>> ; Output control
>> nstxout  = 0; frequency to write coordinates to
>> output trajectory file [steps]
>> nstvout  = 0; frequency to write velocities to
>> output trajectory file  [steps]
>> nstfout  = 0; frequency to write forces to
>>output
>> trajectory file  [steps]
>> nstlog   = 500  ; frequency to write energies to log
>> file [steps]
>> nstenergy= 500  ; frequency to write energies to
>>energy
>> file [steps]
>> nstxtcout= 000 ; frequency to write coordinates to
>>xtc
>> trajectory [steps]
>> xtc-precision= 1000 ; precision to write to xtc
>>trajectory
>> [real]
>> xtc_grps = SOL
>> energygrps   = SOL
>> 
>>;
>>-;
>> 
>>;
>>-;
>> ; Neighborsearching and short-range nonbonded interactions
>> nstlist  = 10   ; frequency to update the neighbor
>>list
>> [steps]
>> ns_type  = grid ; (grid / simple) search for
>> neighboring list
>> pbc  = xyz  ; priodic boundary conditions (xyz
>>/ no
>> / xy)
>> r