[gmx-users] umberlla sampling

[Ali Mohyeddin]

Dear Justin,

In the tutorial of "umbrella sampling
",
what happens if we set the pull_coord1_rate to zero value? Does it work
like a harmonic force (spring) between two groups with a constant distance
averagely?  Indeed, I need to fix the distance between two groups and then
start to pull them.

;Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Ypull_coord1_rate= 0
; 0 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coor1_start= yes   ; define initial COM distance >0

Best regards,

Ali Mohyeddin
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Re: [gmx-users] Temperature dependence of virial of an initial configuration

[Justin Lemkul]

On 3/17/16 11:50 AM, rakesh sharan wrote:

Dear all,

I have a question regarding computation of different components of virial of
my starting initial configuration using Gromacs. When I am running job by
setting nstep  = 0 (system is bulk spce water) to get potential energy and


Note that doing a run with zero steps is not a true single point evaluation.

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy


components of virial of my starting configuration, I am observing that output
components of virial are strongly temperature dependent, even though
potential energy is fixed. This is very surprising to me, as one would expect
that both energy and virial of a starting configuration should be independent
of temperature. I would highly appreciate any thought over this temperature
dependent virial of my initial configuration. I would also appreciate very
much if you could suggest any robust way to get the contribution of virial to
the total pressure of a given configuration.



Manual section A.1 describes the virial computation in detail.

-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] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

[Poncho Arvayo Zatarain]

Hello: i'm running the grompp of NVT but during the run i have the 
following:NOTE: You are applying a switch function to vdw forces or potentials 
from 0 to 1.2 nm, which is more than half the interaction ranges whereas switch 
functions are intended to act only close to the cut-offWhat does it means? it' 
ś anything wrong?My rlist, rcoulomb and rvdw are 1.2 (in nm), vdwtype: cut-off, 
vdwmodifier: force-switch, coulombtype: PME. Should i decrease rlist, rcoulomb 
and rvdw? increase my rlist to 1.4? or change my vdwtype to switch?
Thanks
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Re: [gmx-users] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

[jkrieger]

The problem is you have not set rvdw-switch and the default value is 0.
You should instead set this to something closer to rvdw such as 1.0

It looks like vdw-modifier: potential shift would be a better choice and
then rdw-switch isn't used.
See
http://manual.gromacs.org/documentation/5.1.1/user-guide/mdp-options.html#van-der-waals
for more details

Best wishes
James

>
> Hello: i'm running the grompp of NVT but during the run i have the
> following:NOTE: You are applying a switch function to vdw forces or
> potentials from 0 to 1.2 nm, which is more than half the interaction
> ranges whereas switch functions are intended to act only close to the
> cut-offWhat does it means? it' ¶ anything wrong?My rlist, rcoulomb and
> rvdw are 1.2 (in nm), vdwtype: cut-off, vdwmodifier: force-switch,
> coulombtype: PME. Should i decrease rlist, rcoulomb and rvdw? increase my
> rlist to 1.4? or change my vdwtype to switch?
> Thanks
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[gmx-users] Volume and boundary Questions

[ANAND AMITKUMAR DHARIA]

Hello,

I have two questions about setting up my box for simulation. Thank you for
any and all input in advance.

1. Is the simulation box dimensions and volume fixed throughout the
simulation (or are they allowed to fluctuate around the set dimensions)?

2. Is it possible to make custom box shapes (hexagonal) for a simulation
run instead of using the gromacs supported box types?

Context on my questions is that I would like to simulate proteins in
restrained nanotubes, where the tubes are the dimensions of the simulation
box (this way the entire system will look continuous with no space, when
periodic boundaries are applied).

Please let me know if I need to clarify further.

Thanks,
AD
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Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[James Starlight]

btwh dont understand clearly the whole methodology

for instance If I have coarse'grained system obtained from the
martinize tool consisted of the 1) many proteins embedded within big
bilayer and at the same time 2) FG full atomistic topology for one
protein (without lipids etc) parametrized via ff wich I am going to
use in subsequent CG to FG conversion- will it be sufficiant for the
succesfull FG- CG- FG conversions of the protein7 So will it be
possible to extract CG protein firstly from the whole CG system via
editconf and that obtain its FG representation using ./initram.sh?

Thanks!!

2016-03-17 17:26 GMT+01:00 James Starlight :
> Yep thanks you are right!
>
> It seems that lacking of the FG topology is real problem here.
> Does the |Reverse transformation| method also require the same input
> data for back to FG representation including innitial FG topology7
>
> Thanks in advance!
>
> J.
>
> 2016-03-17 17:20 GMT+01:00  :
>> Hi James,
>> From the tutorial I sent you:
>> To run the script we need the following:
>>
>> The CG structure to backmapp, provided in CG_posre.gro - The CG structure 
>> you want to back map.
>>
>> A complete fine-grained force field corresponding to all the CG molecules in 
>> CG_posre.gro. Here we use CHARMM36, see all .itp files provided and 
>> topol.top, which contains the molecules in the same order they are present 
>> in CG_posre.gro and with the same names. Note, water and ions can be skipped 
>> in the .top files as they are automatically detected by backward.py. - An AA 
>> topology of your system (*itp and *top files in an AA representation).
>>
>> A .map file in the Mapping directory for all residues and molecules to be 
>> backmapped (water and ions can also be skipped here as their definitions are 
>> included in backward.py). - A mapping file that will be use to reconstruct 
>> your CG structure to a FG one based on the topology.
>>
>> According to this, is not posible to reconstruct your system without the FG 
>> topology.
>>
>>
>> --
>>
>> Carlos Navarro Retamal
>> Ingeniero en Bioinformática
>> Ph. D (c) en Ciencias Aplicadas.
>> Centro de Bioinformática y Simulación Molecular
>> Universidad de Talca
>> Av. Lircay S/N, Talca, Chile
>> T: (+56) 712201 798
>> E: carlos.navarr...@gmail.com o cnava...@utalca.cl
>>
>> On March 17, 2016 at 1:12:47 PM, James Starlight (jmsstarli...@gmail.com) 
>> wrote:
>>
>> what I have found from the
>> ./initram.sh -h
>>
>> -f Input coarse grained structure
>> *FILE: None
>> -p Input atomistic target topology
>> *FILE: None
>>
>>
>> does it means that -p should be full atomic topology of the system
>> (not coarse grained) ? Is so whether is possible to make such CG to FG
>> conversion having only CG input data
>>
>> 2016-03-17 17:04 GMT+01:00 James Starlight :
>>> Just tested the ./initram.sh script embedded within the
>>>
>>> Unfortunatelly for my case It didnt works
>>>
>>> 1- I firstly extract the gro file consisted of the protein CG
>>> representation only from my Cg.gro using below command and selecting
>>> protein group
>>> g_editconf -f system.gro -n -o protein.gro
>>>
>>> than I edit my topology putting here only protein itp
>>>
>>> #include "./params/martini_v2.1.itp"
>>> #include "./params/D2.itp"
>>>
>>> [ system ]
>>> Single Low D2
>>>
>>> [ molecules ]
>>> D2 1
>>>
>>>
>>> finally than I apply script on those two files
>>> ./initram.sh -f protein.gro -o aa_charmm.gro -to charmm36 -p protein.top
>>>
>>>
>>> obtaining error
>>>
>>> ---
>>> Program g_grompp, VERSION 4.5.7
>>> Source code file:
>>> /builddir/build/BUILD/gromacs-4.5.7/src/kernel/grompp.c, line: 523
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (0-backward.gro, 0)
>>> does not match topology (backmapped.top, 598)
>>> For more information and tips for troubleshooting, please check the GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> ---
>>>
>>> 2016-03-17 16:24 GMT+01:00 James Starlight :
 Is it better than
 http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
 7 PArticularly for my case I need to convert from CG to FG the
 structure of GPCR simulated within CG lipids excluding lipids in the
 final FG model.

 2016-03-17 15:49 GMT+01:00 :
> Hi James,
> There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to 
> reconstruct the atomistic structure from a CG structure.
> Here is the respective tutorial 
> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward
>  (from the MARTINI group), and here is the paper of the back mapping 
> method:
> http://pubs.acs.org/doi/abs/10.1021/ct400617g
> Hope this helps.
> Best,
> Carlos
> --
>
> Carlos 

[gmx-users] pull code for Gromacs 5

[Nash, Anthony]

Hi all,

I¹m very unfamiliar with the pull code as of Gromacs 5. Unfortunately my
system is not experiencing any noticeable Œpull¹. From the options below,
which is the group experiencing the pull and which is the reference group?
 Would applying a set of position restraints on the reference group
prevent (in theory) the pulling group to move? From someone only having
ran pull code on earlier versions of gromacs, am I missing anything
blindingly obvious?


pull= umbrella
pull-geometry   = direction-periodic
pull-dim= N N Y
pull-start  = yes
pull-ncoords= 1
pull-ngroups= 2
pull-group1-name= fix_collagen
pull-group1-pbcatom = 0
pull-group2-name= pull_group
pull-coord1-groups  = 1 2
pull-coord1-rate= 0.1
pull-coord1-k   = 1000



Context: I am pulling an explicit collagen molecule away from its
neighbour. They are in a very tight Œrectangle¹, thus they are
experiencing a pseudo fibril environment. The need for direction-periodic
is due to the length I am pulling the molecule (past half the box size).

Thanks
Anthony



Dr Anthony Nash
Department of Chemistry
University College London



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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Pradip Kaur]

actually i m not getting how to proceed futher i m beginner to GROMACS
it would be helpful if you can elaborate the process

On 17 March 2016 at 21:54, Pradip Kaur  wrote:

> so should i go for sol molecules :1612
>  Na :11
>
> On 17 March 2016 at 21:44, Peter Stern  wrote:
>
>> Missing atoms in GLU 474 is because the coordinates for the GLU side
>> chain weren't resolved in the crystallographic data and aren't included in
>> the pdb file.  Long bonds are probably because of missing residues.  Check
>> the pdb file for MISSING residues and atoms (listed in the header
>> records).  Also, you can't just delete a residue and let Gromacs think that
>> the preceding and following residues are connected (by an unphysical "long"
>> bond).  The same goes for missing residues in the pdb file.
>>
>> I hope that the net charge was -5.999 otherwise, why add Na ions.  And as
>> far as I know, 11*1612=17732.
>>
>> Peter Stern
>>
>> Sent from my iPad
>>
>> On 17 במרץ 2016, at 11:08, Pradip Kaur  kaur.pradip...@gmail.com>> wrote:
>>
>> i am currently working with 2bbo.pdb protein ,i have edited this protein
>> in
>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now i m
>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after running
>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
>> showing
>>
>> Warning: Long Bond (161-163 = 1.78456 nm)
>>
>> Warning: Long Bond (840-842 = 0.357037 nm)
>>
>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>>
>>
>>
>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>>
>>
>>
>>
>>
>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
>>
>>
>>
>>
>>
>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
>>
>>
>>
>>
>>
>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
>>
>>
>>
>>
>>
>> ---
>>
>> Program pdb2gmx, VERSION 5.0.2
>>
>> Source code file:
>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
>> 1587
>>
>>
>>
>> Fatal error:
>>
>> There were 4 missing atoms in molecule Protein_chain_A, if you want to use
>> this incomplete topology anyhow, use the option -missing
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> *But  after ignoring missing atoms ,when i am running grompp command it
>> shows that the system has non zero integral charge of 5.999.*
>>
>> *i have added command genion to neutalise the charge by adding 6 Na ions
>> .After running the command it says that you have generated 17732 solvent
>> molecules which are not multiple of 11 .*
>>
>> *can any one help me with this problem*
>> --
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>
>
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Re: [gmx-users] Potential energy of each atom

[Josip Lovrić]

Potential energy for one atom is not well defined physical quantity as far
as I know, you can only calculate potential energy for at least two body
(atoms). You need to give more details about what you want and I do not
know what LAMMPS do.

Josip

2016-03-18 11:03 GMT+01:00 张正财 :

> > Subject: Re: [gmx-users] Potential energy of each atom
> > Message-ID: <56eba4a9.8020...@xray.bmc.uu.se>
> > Content-Type: text/plain; charset=UTF-8; format=flowed
> >
> > On 18/03/16 03:40, ??? wrote:
> > > Dear all,
> > >
> > >Could anyone tell me how can I output potential energy of each
> atom from a trajectory file?
> > >
> > What does that mean?
>
> Like the command in LAMMPS, "compute pe/atom", I want to display the
> potential energy of each atom in simulation system. is it possible in
> gromacs?
> >
> > If you have a Na+ and a Cl- in the gas phase Gromacs can compute Coulomb
> > energy and Lennard Jones energy. But how would you partition that over
> > atoms?
> >
> >
> >
> > >All the best,
> > >
> > >   Zhengcai
> > >
> > >  Iggcas, CAS
> > >
> > >
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> >
> >
>
>
>
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 80

[Soumya Lipsa Rath]

Dear Justin,

Thanks for your reply. I meant, that the PRODRG server gave error in giving
the topology file since my inhibitor contains a metal which the server
doesn't process. If PRODRG is meant for GROMOS, should I use CGENFF for
CHARMM? In that case, how do we include the topology of the inhibitor
during the protein-ligand simulation?

Thanks,
Soumya

>
>
> On 3/16/16 10:18 PM, Soumya Lipsa Rath wrote:
> > Dear Gromacs Users,
> >
> > I have to run a protein-ligand system. I am using CHARMM36 ff for the
> > simulation. For generating the parameters for the ligand molecule I used
> > the forcefield development toolkit of vmd, which gives CHARMM compatible
> > parameters.
> >
> > But, I am unable to understand how should I include the parameters I had
> > obtained. I went through the tutorial files which shows an example of
> > PRODRG server for generating the itp file, but my ligand contains metal
> > atoms. I would appreciate if somebody could suggest me how to solve this.
> >
>
> What are the ligands?  What metal?
>
> Don't use PRODRG; it's only intended for GROMOS force fields (and even
> then, the
> topologies need a lot of work).
>
> -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] Domain decomposition error tied to free energy perturbation

[Ryan Muraglia]

On Fri, Mar 18, 2016 at 7:47 AM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
>
> Message: 4
> Date: Fri, 18 Mar 2016 07:46:48 -0400
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Domain decomposition error tied to free
> energy perturbation
> Message-ID: <56ebeaa8.1050...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 3/17/16 8:21 PM, Ryan Muraglia wrote:
> > Hello,
> >
> > I have been attempting to carry out some free energy calculations, but to
> > verify the sanity of my parameters, I decided to test them on a
> structure I
> > knew to be stable -- the lysozyme from Lemkul's lysozyme in water
> tutorial.
> >
> > I chose the L75A mutation because it is out on the surface to minimize
> the
> > "difficulty of the transformation."
> > Using my regular mdp file (even with my mutatation topology generated
> with
> > the pmx package), my minimization runs to completion with no errors.
> >
> > Once I introduce the following lines to my mdp file:
> >
> > "
> > ; Free energy calculations
> > free_energy = yes
> > delta_lambda = 0 ; no Jarzynski non-eq
> > calc_lambda_neighbors = 1 ; only calculate energy to immediate neighbors
> > (suitable for BAR, but MBAR needs all)
> > sc-alpha = 0.5
> > sc-coul  = no
> > sc-power = 1.0
> > sc-sigma = 0.3
> > couple-moltype   = Protein_chain_A  ; name of moleculetype to
> > decouple
> > couple-lambda0   = vdw-q  ; all interactions
> > couple-lambda1   = vdw ; remove electrostatics, only vdW
> > couple-intramol  = no
> > nstdhdl  = 100
> >
> > ; lambda vectors ; decharging only.
> > ; init_lambda_state   0   1   2   3   4   5   6   7   8   9   10
> > init_lambda_state = 00
> > coul_lambdas =0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
> > vdw_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
> > bonded_lambdas =  0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; match
> > vdw
> > mass_lambdas =0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; match
> > vdw
> > temperature_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; not
> > doing simulated tempering
> > "
> >
> > I notice two things:
> > 1) Running grompp to generate the tpr file takes much longer
> > 2) The minimization fails to run due the following error related to
> domain
> > decomposition:
> >
> > "
> > Fatal error:
> > There is no domain decomposition for 4 ranks that is compatible with the
> > given box and a minimum cell size of 5.51109 nm
> > Change the number of ranks or mdrun option -rdd
> > Look in the log file for details on the domain decomposition
> > "
> >
> > I noted that it lists a two-body bonded interaction with a strangely
> large
> > distance:
> >
> > "
> > Initial maximum inter charge-group distances:
> >  two-body bonded interactions: 5.010 nm, LJC Pairs NB, atoms 1074
> 1937
> >multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1156 1405
> > Minimum cell size due to bonded interactions: 5.511 nm
> > "
> >
> > Atom 1074 corresponds to a hydrogen off the beta-carbon of proline 70,
> and
> > atom 1937 refers to a hydrogen on arginine 128. Neither residue is part
> of
> > the protein that is being mutated, and they certainly should not be
> bonded.
> > The [bonds] directive in the topology confirms that there should be no
> > interaction between these atoms.
>
> With "couple-intramol = no" (from the manual):
>
> "All intra-molecular non-bonded interactions for moleculetype
> couple-moltype are
> replaced by exclusions and explicit pair interactions."
>
> So you have a much larger distance for intramolecular interactions, hence
> DD
> complains and you are more limited in the number of DD cells that can be
> constructed.  Trying to decouple an entire protein chain is (1) not usually
> reasonable and (2) fraught with algorithmic challenges.
>
> > To force the run to begin to get more information on the nature of the
> > error, I gave mdrun the -nt 1 option, and got the following warning at
> the
> > beginning of the minimization (which goes on to end prematurely prior to
> > reaching the desired Fmax):
> >
> > "
> > WARNING: Listed nonbonded interaction between particles 1 and 195
> > at distance 2.271 which is larger than the table limit 2.200 nm.
> > "
> >
> > I'm at a loss in terms of understanding why the addition of my FEP
> > parameters is causing this error, and appears to be causing the grompp
> > parser to decide that there is a bond where there shouldn't be, forcing
> the
>
> It's not magically creating bonds; see above.  grompp is taking forever
> because
> it has to generate a massive list of exclusions and pairs.
>
> > minimimum box size to exceed what makes sense for domain decomposition.
> >
>
> If EM fails, that's usually a dead giveaway that either the topology is
> unsound
> or the initial coordinates are 

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Peter Stern]

Missing atoms in GLU 474 is because the coordinates for the GLU side chain 
weren't resolved in the crystallographic data and aren't included in the pdb 
file.  Long bonds are probably because of missing residues.  Check the pdb file 
for MISSING residues and atoms (listed in the header records).  Also, you can't 
just delete a residue and let Gromacs think that the preceding and following 
residues are connected (by an unphysical "long" bond).  The same goes for 
missing residues in the pdb file.

I hope that the net charge was -5.999 otherwise, why add Na ions.  And as far 
as I know, 11*1612=17732.

Peter Stern

Sent from my iPad

On 17 במרץ 2016, at 11:08, Pradip Kaur 
> wrote:

i am currently working with 2bbo.pdb protein ,i have edited this protein in
Discovery studio 4.5 and deleted phenylalanine at 508 position , now i m
running molecular dynamics simulation  in GROMACS 5.0.2 bt after running
pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is showing

Warning: Long Bond (161-163 = 1.78456 nm)

Warning: Long Bond (840-842 = 0.357037 nm)

Warning: Long Bond (2237-2239 = 0.636287 nm)



WARNING: atom CG is missing in residue GLU 474 in the pdb file





WARNING: atom CD is missing in residue GLU 474 in the pdb file





WARNING: atom OE1 is missing in residue GLU 474 in the pdb file





WARNING: atom OE2 is missing in residue GLU 474 in the pdb file





---

Program pdb2gmx, VERSION 5.0.2

Source code file:
/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1587



Fatal error:

There were 4 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology anyhow, use the option -missing

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors


*But  after ignoring missing atoms ,when i am running grompp command it
shows that the system has non zero integral charge of 5.999.*

*i have added command genion to neutalise the charge by adding 6 Na ions
.After running the command it says that you have generated 17732 solvent
molecules which are not multiple of 11 .*

*can any one help me with this problem*
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Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[carlos . navarro87]

Hi James,
From the tutorial I sent you:
To run the script we need the following:

The CG structure to backmapp, provided in CG_posre.gro - The CG structure you 
want to back map.

A complete fine-grained force field corresponding to all the CG molecules in 
CG_posre.gro. Here we use CHARMM36, see all .itp files provided and topol.top, 
which contains the molecules in the same order they are present in CG_posre.gro 
and with the same names. Note, water and ions can be skipped in the .top files 
as they are automatically detected by backward.py. - An AA topology of your 
system (*itp and *top files in an AA representation). 

A .map file in the Mapping directory for all residues and molecules to be 
backmapped (water and ions can also be skipped here as their definitions are 
included in backward.py). - A mapping file that will be use to reconstruct your 
CG structure to a FG one based on the topology.

According to this, is not posible to reconstruct your system without the FG 
topology.


-- 

Carlos Navarro Retamal
Ingeniero en Bioinformática
Ph. D (c) en Ciencias Aplicadas.
Centro de Bioinformática y Simulación Molecular
Universidad de Talca
Av. Lircay S/N, Talca, Chile 
T: (+56) 712201 798
E: carlos.navarr...@gmail.com o cnava...@utalca.cl

On March 17, 2016 at 1:12:47 PM, James Starlight (jmsstarli...@gmail.com) wrote:

what I have found from the
./initram.sh -h

-f Input coarse grained structure
*FILE: None
-p Input atomistic target topology
*FILE: None


does it means that -p should be full atomic topology of the system
(not coarse grained) ? Is so whether is possible to make such CG to FG
conversion having only CG input data

2016-03-17 17:04 GMT+01:00 James Starlight :
> Just tested the ./initram.sh script embedded within the
>
> Unfortunatelly for my case It didnt works
>
> 1- I firstly extract the gro file consisted of the protein CG
> representation only from my Cg.gro using below command and selecting
> protein group
> g_editconf -f system.gro -n -o protein.gro
>
> than I edit my topology putting here only protein itp
>
> #include "./params/martini_v2.1.itp"
> #include "./params/D2.itp"
>
> [ system ]
> Single Low D2
>
> [ molecules ]
> D2 1
>
>
> finally than I apply script on those two files
> ./initram.sh -f protein.gro -o aa_charmm.gro -to charmm36 -p protein.top
>
>
> obtaining error
>
> ---
> Program g_grompp, VERSION 4.5.7
> Source code file:
> /builddir/build/BUILD/gromacs-4.5.7/src/kernel/grompp.c, line: 523
>
> Fatal error:
> number of coordinates in coordinate file (0-backward.gro, 0)
> does not match topology (backmapped.top, 598)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> 2016-03-17 16:24 GMT+01:00 James Starlight :
>> Is it better than
>> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
>> 7 PArticularly for my case I need to convert from CG to FG the
>> structure of GPCR simulated within CG lipids excluding lipids in the
>> final FG model.
>>
>> 2016-03-17 15:49 GMT+01:00 :
>>> Hi James,
>>> There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to 
>>> reconstruct the atomistic structure from a CG structure.
>>> Here is the respective tutorial 
>>> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward
>>>  (from the MARTINI group), and here is the paper of the back mapping method:
>>> http://pubs.acs.org/doi/abs/10.1021/ct400617g
>>> Hope this helps.
>>> Best,
>>> Carlos
>>> --
>>>
>>> Carlos Navarro Retamal
>>> Ingeniero en Bioinformática
>>> Ph. D (c) en Ciencias Aplicadas.
>>> Centro de Bioinformática y Simulación Molecular
>>> Universidad de Talca
>>> Av. Lircay S/N, Talca, Chile
>>> T: (+56) 712201 798
>>> E: carlos.navarr...@gmail.com o cnava...@utalca.cl
>>>
>>> On March 17, 2016 at 11:07:48 AM, James Starlight (jmsstarli...@gmail.com) 
>>> wrote:
>>>
>>> Dear Gromacs users!
>>>
>>> I wonder to ask for some suggestions about possibility of the CG to
>>> full atomistic conversion of sample pdb files extracted from the CG
>>> (Martini based) md trajectories. I will be especially thankful for any
>>> kind of the useful tutorial focused on the subject.
>>>
>>> Thanks for help in advance!
>>>
>>> J.
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at 
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>>>
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>>>
>>> * Please search the archive at 
>>> 

[gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps

[Poncho Arvayo Zatarain]

Hello. I' ḿ simulating a DPPC membrane with TIP3 water model and charmm36 
forcefield and in the grompp of NVT equilibration i have this warning: (Warning 
1: file topol.top line 24) The bond in molecular type DPPC between atoms 31 C21 
y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less 
than 5 times the time step of 1.0e-01 ps. Maybe you forgot to change the 
constraints mdp option. What can i do to solve this? I attached mu nvt.mdp and 
topol.top. Also i have Note 1: rlist is equal to rvdw or/and rcoulomb. There is 
no explicit verlet buffer. The cluster pair list does have a buffering effect, 
but choosing a larger rlist might be neccesari for good energy 
conservation.Note 2: nstcommhttp://www.charmm-gui.org) v1.7 
psf2itp.py Correspondance:;; j712l...@ku.edu or won...@ku.edu The main 
GROMACS topology file;;
; Include forcefield parameters#include "toppar/charmm36.itp"#include 
"toppar/DPPC.itp"#include "toppar/TIP3.itp"
[ system ]; NameTitle
[ molecules ]; Compound #molsDPPC256TIP38896
  
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Re: [gmx-users] Hydrogen bonding pair selection (Erik Marklund)

[Binwu Zhao]

Dear Eric,

You are right, it doesn’t cause any problems with the results! 

Thanks a lot!
Binwu

> On Mar 17, 2016, at 5:18 PM, 
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
> 
> 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
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> or, via email, send a message with subject or body 'help' to
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> 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. Re: creating representative structures (Tsjerk Wassenaar)
>   2. pull code for Gromacs 5 (Nash, Anthony)
>   3. Volume and boundary Questions (ANAND AMITKUMAR DHARIA)
>   4. Hydrogen bonding pair selection (Binwu Zhao)
>   5. Re: Hydrogen bonding pair selection (Erik Marklund)
> 
> 
> --
> 
> Message: 1
> Date: Thu, 17 Mar 2016 18:36:02 +0100
> From: Tsjerk Wassenaar 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] creating representative structures
> Message-ID:
>   
> Content-Type: text/plain; charset=UTF-8
> 
> Hi Shyno,
> 
> Is there a difference in mass-weighting? Can you try on C- alphas only?
> 
> Cheers,
> 
> Tsjerk
> On Mar 16, 2016 15:55, "Shyno Mathew"  wrote:
> 
>> Dear all,
>> 
>> 
>> I wrote a tcl script to do cluster analysis, using gromos method. My
>> results are slightly different from the g_cluster results. I see the
>> difference is coming from RMSD values. For example, with g_cluster, ?The
>> RMSD ranges from 0.149614 to 0.220387 nm?
>> 
>> 
>> However with the tcl script, and after converting RMSD from ? to nm, the
>> value ranges from 0.173347 to 0.234409 nm! I am using the same selection in
>> both cases for RMSD calculations.
>> 
>> 
>> I use g_cluster the following way:
>> 
>> g_cluster_mpi ?s ../PRO0.gro -f ../comb6.xtc -method gromos -sz
>> clustsize.xvg -o clusters.xpm -g cluster.log -clid clusidovertime.xvg -cl
>> -av out.pdb -cutoff 0.20 -dist rmsd-dist.xvg
>> 
>> 
>> For vmd, I use PRO0.gro, comb6.xtc and I am not considering the 0th frame,
>> so the RMSD values from both cases has to be identical.
>> 
>> 
>> thanks,
>> 
>> Shyno
>> 
>> On Mon, Feb 29, 2016 at 6:52 PM, Shyno Mathew  wrote:
>> 
>>> Dear all,
>>> 
>>> I was able to write a tcl script to do cluster analysis, here I am using
>>> the gromos method.
>>> However, my script is giving slightly different results! I am testing my
>>> script on a smaller trajectory (8 frames).
>>> In the gromos method, the structure with the greatest number of neighbors
>>> is considered as the center of the cluster.
>>> What if more than one structure has the highest number of neighbors. For
>>> example, in my calculation, both frames 4 and 6 has 6 neighbors (maximum
>>> neighbor count).
>>> When I used g_cluster, the output file shows cluster center as frame 6.
>>> That means if I have more than one structure that has the maximum number
>> of
>>> neighbors, I can randomly choose the cluster center?
>>> 
>>> thanks,
>>> Shyno
>>> 
>>> 
>>> On Fri, Feb 26, 2016 at 11:47 AM, Shyno Mathew 
>>> wrote:
>>> 
 Dear Prof. Mark and Prof. Stephane,
 
 Thanks so much for your suggestions.
 
 thanks,
 Shyno
 
 On Mon, Feb 8, 2016 at 12:23 PM, Shyno Mathew 
 wrote:
 
> Dear all,
> 
> 
> I have few questions regarding creating representative structures. For
> simplicity, let?s say I have a trajectory of 5 frames:
> 
> 1.   g_rmsf: After reading previous posts, here is what I
> understood. The average structures calculated using g_rmsf (by
>> specifying
> ?ox) is literally the average of x, y, z co-ordinates of each atom
>> over all
> the 5 frames in my case. Energy minimizing this averaged structure
>> might
> give a meaningful structure?
> 
> 2.   g_cluster: Here I am using the gromos method. I read the
> reference paper (Daura et al.). Using gromos method and by just
>> specifying
> ?cl (not ?av) I get the middle structures for each cluster. Let?s say
>> I get
> 2 clusters using rmsd 0.16. Now the representative structures of these
>> two
> clusters (obtained in the out.pdb) should exactly correspond to two
>> frames
> in my original trajectory (the one with 5 frames)?
> 
> 3.   My final question is regarding how exactly g_cluster works,
> here is what I understand from Daura et al.
> 
> If I use g_cluster with 

[gmx-users] LINCS warnings for some lambdas.

[Sana Saeed]

hii am performing protein ligand (pdb:4HBV)binding free energy calculations, i 
am done with complex simulation , now stuck in ligand simulation since last 2 
weeks. first i was getting zero energy, and when i changed some of parameters 
and position restraint my ligand , now i am getting LINCS warnings sometimes 
with NPT  and sometimes during production md. the strange part is that some of 
the lambdas are perfectly running while some of them crashes due to LINCS 
warnings, i know how to fix LINCS warnings (extending table size, decreasing 
stepsize, properly minimizing structure etc) but in  this case some of lambdas 
are running perfectly, which means the structure and parameters are fine. i 
decresed step size to 1 fs and got the same result, bow i decreased it to 
0.0001 ps. if someone ever got this kind of problem , please share your views. 
my second question is that the simple simulation for solvation free energy of 
small molecule and the ligand simulation in binding free energy system are 
same? i mean can i use the solvation free energy parameters from BEVAN lab's 
tutorial in this situation? in some of tutorials they use position restraints 
for ligand simulation in water, that is the reason i used the same. i provide 
npt and md.mdp parameters. if something is wrong kindly give comments. ignore 
the stepsize , i know its too small, i tried 0.001, 0.002, and this is the 
recent one, but couldnt see any difference.thanks in advance 
NPT.mdp
define              =  -DPOSRESintegrator          =  sdtinit               =  
0dt                  =  0.0001   nsteps              =  50  ; 100 psnstcomm 
            =  100
; Boundary conditionspbc                 =  xyz
; Outputnstxout             =  0nstvout             =  0nstfout             =  
0nstlog              =  100   ; 10 psnstenergy           =  100   ; 10 
psnstcalcenergy       =  20nstxtcout           =  100   ; 10 psxtc-precision    
   =  1000energygrps          =  System
; Neighbour searchingcutoff-scheme       = Verletnstlist             = 10      
; 20 fsns-type             = gridrlist               = 1.2               ; 
short-range neighborlist cutoff (in nm)rcoulomb            = 1.2               
; short-range electrostatic cutoff (in nm)rvdw                = 1.2             
  ; short-range van der Waals cutoff (in nm)
; Constraintsconstraints         =  noneconstraint-algorithm = lincslincs_iter  
        = 1         ; accuracy of LINCS (1 is default)lincs_order         = 12  
      ; also related to accuracy (4 is default)lincs-warnangle     = 30        
; maximum angle that a bond can rotate before LINCS will complain^M; 
Electrostaticscoulombtype     = PME           ; Particle Mesh Ewald for 
long-range electrostaticspme-order       = 6             fourierspacing  = 0.10 
         ; grid spacing for FFTewald-rtol      = 1e-6          ; relative 
strength of the Ewald-shifted direct potential at rcoulomboptimize-fft    = 
noewald_geometry   = 3d  
; van der Waal'svdwtype            =  Switchrvdw-switch         =  0.9DispCorr  
          =  EnerPres
;Temperature Coupling (SD integrator => Langevin dynamics)tc_grps             = 
 Systemtau_t               =  1.0ref_t               =  298.15
; Pressure couplingPcoupl              =  Berendsenpcoupltype          =  
isotropictau_p               =  2compressibility     =  4.5e-05ref_p            
   =  1.0
; Generate velocitiesgen_vel             = yesgen_seed            = -1gen_temp  
          = 298.15
continuation        = no 
; Free energy control stuff = free-energy              = yessc-alpha            
     = 0.5sc-power                 = 1sc-sigma                 = 
0.3init-lambda-state        = 0coul-lambdas             = 0.0 0.1 0.2 0.3 0.4 
0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 
1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0vdw-lambdas              = 0.0 0.0 0.0 0.0 
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 
0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0  couple-moltype          = 15E 
couple-intramol         = no couple-lambda0          = none couple-lambda1      
    = vdw-qnstdhdl                  = 100calc-lambda-neighbors    = 
-1refcoord-scaling         = com
PRODUCTION MD:md.mdp
; Production MD;title           = production
; Run parametersintegrator      = sd            ; stochastic leap-frog 
integratornsteps          = 250       dt              = 0.0001              
  nstcalcenergy   =  100energygrps      =  System
; Periodic boundary conditionspbc             = xyz           ; 3-D PBC
; Output controlnstvout         = 500        ; save velocities to .trr file 
every 200 psnstfout         = 500        ; save forces to .trr file every 100 
psnstxout         = 500           ; save coordinates every 5 psnstxtcout       
= 500           ; xtc compressed trajectory output every 2 psnstenergy       = 
500           ; save energies every 2 psnstlog          = 500           ; 
update log file every 2 

Re: [gmx-users] Volume and boundary Questions

[Justin Lemkul]

On 3/17/16 3:01 PM, ANAND AMITKUMAR DHARIA wrote:

Hello,

I have two questions about setting up my box for simulation. Thank you for
any and all input in advance.

1. Is the simulation box dimensions and volume fixed throughout the
simulation (or are they allowed to fluctuate around the set dimensions)?



That depends on the ensemble you choose for the simulation.  NVT = fixed box 
size.  NPT = the box size varies in response to pressure.



2. Is it possible to make custom box shapes (hexagonal) for a simulation
run instead of using the gromacs supported box types?



If it's not supported, it's not supported.

-Justin


Context on my questions is that I would like to simulate proteins in
restrained nanotubes, where the tubes are the dimensions of the simulation
box (this way the entire system will look continuous with no space, when
periodic boundaries are applied).

Please let me know if I need to clarify further.

Thanks,
AD



--
==

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

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

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

==
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 80

[Justin Lemkul]

On 3/17/16 8:04 PM, Soumya Lipsa Rath wrote:

Dear Justin,

Thanks for your reply. I meant, that the PRODRG server gave error in giving
the topology file since my inhibitor contains a metal which the server
doesn't process. If PRODRG is meant for GROMOS, should I use CGENFF for
CHARMM? In that case, how do we include the topology of the inhibitor
during the protein-ligand simulation?



Yes, you should use CGenFF when using the CHARMM force field.  They're 
compatible by design.


But I can't guarantee that you'll even be able to create a topology; CGenFF is 
for organic molecules.  Any metal parameters would have to come from CHARMM 
itself, but you still haven't told me what that metal is so I don't know if 
CHARMM will cover it...


-Justin


Thanks,
Soumya




On 3/16/16 10:18 PM, Soumya Lipsa Rath wrote:

Dear Gromacs Users,

I have to run a protein-ligand system. I am using CHARMM36 ff for the
simulation. For generating the parameters for the ligand molecule I used
the forcefield development toolkit of vmd, which gives CHARMM compatible
parameters.

But, I am unable to understand how should I include the parameters I had
obtained. I went through the tutorial files which shows an example of
PRODRG server for generating the itp file, but my ligand contains metal
atoms. I would appreciate if somebody could suggest me how to solve this.



What are the ligands?  What metal?

Don't use PRODRG; it's only intended for GROMOS force fields (and even
then, the
topologies need a lot of work).

-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

==






--
==

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] You are applying a switch function to vdw forces or potentials from 0 to 1.2 nm

[Mark Abraham]

Hi,

Like it says, you've somehow chosen for a switching radius to start at 0
nm, which you likely did not intend nor should do. Consider your recent
changes.

Mark

On Thu, 17 Mar 2016 17:46 Poncho Arvayo Zatarain 
wrote:

>
> Hello: i'm running the grompp of NVT but during the run i have the
> following:NOTE: You are applying a switch function to vdw forces or
> potentials from 0 to 1.2 nm, which is more than half the interaction ranges
> whereas switch functions are intended to act only close to the cut-offWhat
> does it means? it' ś anything wrong?My rlist, rcoulomb and rvdw are 1.2 (in
> nm), vdwtype: cut-off, vdwmodifier: force-switch, coulombtype: PME. Should
> i decrease rlist, rcoulomb and rvdw? increase my rlist to 1.4? or change my
> vdwtype to switch?
> Thanks
> --
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[gmx-users] simulation a box of water

[Saeed Nasiri]

Dear all

I want to simulate a box of water (2*2*2 nm with 1401 molecules). Is there
difference between using a model for water molecules and importing this
molecule from other programs(such as nwchem)?
I want to do a small simulation and it is not important to treat water
molecules explicitly.
I used a water.pdb file to generate the box with this command:


*gmx_mpi insert-molecules -ci WATER.pdb -nmol 3000 -box 2 2 2 -o
water_box.gro*
 ...
 
Added 467 molecules (out of 3000 requested)
Writing generated configuration to water_box.gro

Output configuration contains 1401 atoms in 934 residues

gcq#247: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix"
(Indeep)

after that I want to create topol.gro file, but I got an error ?


*gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh*
  :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
Kutzner
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx_mpi
Data prefix:  /usr/local/gromacs
Command line:
  gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh


Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat

Select the Water Model:
 1: TIP4P  TIP 4-point, recommended
 2: TIP4PEW TIP 4-point with Ewald
 3: TIP3P  TIP 3-point
 4: TIP5P  TIP 5-point (see http://redmine.gromacs.org/issues/1348 for
issues)
 5: TIP5P  TIP 5-point improved for Ewald sums
 6: SPCsimple point charge
 7: SPC/E  extended simple point charge
 8: None
8
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading water_box.gro...
Read 'UNNAMED', 467 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 0 chains and 1 blocks of water and 934 residues with 467 atoms

  chain  #res #atoms
  1 ' '   933467  (only water)

No occupancies in water_box.gro
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 814
Reading residue database... (oplsaa)
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 52
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.1#
Processing chain 1 (467 atoms, 933 residues)
Problem 

Re: [gmx-users] simulation a box of water

[Justin Lemkul]

On 3/16/16 12:00 PM, Saeed Nasiri wrote:

thanks so much for all the comments.

as far as I know the water molecules created by models have solid bods and
angles. I want to extract thermodynamical parameters from the simulation,
for this purpose I used this method.
Is this a trick to used water molecule explicitly?


If I understand the question, you simply want to carry out a simulation of 
flexible water?  You still need to choose a water model (for charges, LJ, and 
bonded parameters) but you can run with "define = -DFLEXIBLE" to avoid the use 
of SETTLE, which keeps the model rigid.  Inspect the contents of any water 
model's .itp file and you will see exactly what's going on.  Moreover, you don't 
need pdb2gmx, because the topology is straightforward to write by hand:


#include (some force field)
#include (the water model's .itp file)

[ system ]
water

[ molecules ]
SOL 3000

That's it.  People tend to get hung up on this idea that you have to use 
pdb2gmx.  That's not true at all, especially for utterly trivial systems like 
this one.


-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] creating representative structures

[Tsjerk Wassenaar]

Hi Shyno,

Is there a difference in mass-weighting? Can you try on C- alphas only?

Cheers,

Tsjerk
On Mar 16, 2016 15:55, "Shyno Mathew"  wrote:

> Dear all,
>
>
> I wrote a tcl script to do cluster analysis, using gromos method. My
> results are slightly different from the g_cluster results. I see the
> difference is coming from RMSD values. For example, with g_cluster, “The
> RMSD ranges from 0.149614 to 0.220387 nm”
>
>
> However with the tcl script, and after converting RMSD from Å to nm, the
> value ranges from 0.173347 to 0.234409 nm! I am using the same selection in
> both cases for RMSD calculations.
>
>
> I use g_cluster the following way:
>
> g_cluster_mpi –s ../PRO0.gro -f ../comb6.xtc -method gromos -sz
> clustsize.xvg -o clusters.xpm -g cluster.log -clid clusidovertime.xvg -cl
> -av out.pdb -cutoff 0.20 -dist rmsd-dist.xvg
>
>
> For vmd, I use PRO0.gro, comb6.xtc and I am not considering the 0th frame,
> so the RMSD values from both cases has to be identical.
>
>
> thanks,
>
> Shyno
>
> On Mon, Feb 29, 2016 at 6:52 PM, Shyno Mathew  wrote:
>
> > Dear all,
> >
> > I was able to write a tcl script to do cluster analysis, here I am using
> > the gromos method.
> > However, my script is giving slightly different results! I am testing my
> > script on a smaller trajectory (8 frames).
> > In the gromos method, the structure with the greatest number of neighbors
> > is considered as the center of the cluster.
> > What if more than one structure has the highest number of neighbors. For
> > example, in my calculation, both frames 4 and 6 has 6 neighbors (maximum
> > neighbor count).
> > When I used g_cluster, the output file shows cluster center as frame 6.
> > That means if I have more than one structure that has the maximum number
> of
> > neighbors, I can randomly choose the cluster center?
> >
> > thanks,
> > Shyno
> >
> >
> > On Fri, Feb 26, 2016 at 11:47 AM, Shyno Mathew 
> > wrote:
> >
> >> Dear Prof. Mark and Prof. Stephane,
> >>
> >> Thanks so much for your suggestions.
> >>
> >> thanks,
> >> Shyno
> >>
> >> On Mon, Feb 8, 2016 at 12:23 PM, Shyno Mathew 
> >> wrote:
> >>
> >>> Dear all,
> >>>
> >>>
> >>> I have few questions regarding creating representative structures. For
> >>> simplicity, let’s say I have a trajectory of 5 frames:
> >>>
> >>> 1.   g_rmsf: After reading previous posts, here is what I
> >>> understood. The average structures calculated using g_rmsf (by
> specifying
> >>> –ox) is literally the average of x, y, z co-ordinates of each atom
> over all
> >>> the 5 frames in my case. Energy minimizing this averaged structure
> might
> >>> give a meaningful structure?
> >>>
> >>> 2.   g_cluster: Here I am using the gromos method. I read the
> >>> reference paper (Daura et al.). Using gromos method and by just
> specifying
> >>> –cl (not –av) I get the middle structures for each cluster. Let’s say
> I get
> >>> 2 clusters using rmsd 0.16. Now the representative structures of these
> two
> >>> clusters (obtained in the out.pdb) should exactly correspond to two
> frames
> >>> in my original trajectory (the one with 5 frames)?
> >>>
> >>> 3.   My final question is regarding how exactly g_cluster works,
> >>> here is what I understand from Daura et al.
> >>>
> >>> If I use g_cluster with gromos method, the code will look for neighbors
> >>> of each frame within specified cutoff.
> >>>
> >>> Assume the first time the code finds the following:
> >>>
> >>> frame 0 has two neighbors: frames 2,3  within cutoff
> >>>
> >>> frame 1 has three neighbors: frames 2, 3, 4 within cutoff
> >>>
> >>> frame 2 has four neighbors: frames 0, 1, 3, 4 within cutoff
> >>>
> >>> frame 3 has three neighbors: frames 0,1, 2 within cutoff
> >>>
> >>> frame 4 has two neighbors: frames 1,2 within cutoff
> >>>
> >>>
> >>>
> >>> Since frame 2 has the highest number of neighbors, it's considered the
> >>> center cluster and this frame along with neighbors are removed. The
> same
> >>> calculation is performed on the remaining frames if I had more frames.
> >>>
> >>>
> >>>
> >>> Thanks in advance for your help,
> >>>
> >>> Sincerely,
> >>>
> >>> Shyno
> >>>
> >>> --
> >>> Shyno Mathew
> >>> PhD Candidate
> >>> Department of Chemical Engineering
> >>> Graduate Assistant
> >>> Office of Graduate Student Affairs
> >>> The Fu Foundation School Of Engineering and Applied Science
> >>> Columbia University
> >>>
> >>
> >>
> >>
> >> --
> >> Shyno Mathew
> >> PhD Candidate
> >> Department of Chemical Engineering
> >> Graduate Assistant
> >> Office of Graduate Student Affairs
> >> The Fu Foundation School Of Engineering and Applied Science
> >> Columbia University
> >>
> >
> >
> >
> > --
> > Shyno Mathew
> > PhD Candidate
> > Department of Chemical Engineering
> > Graduate Assistant
> > Office of Graduate Student Affairs
> > The Fu Foundation School Of Engineering and Applied Science
> > Columbia University
> >
>
>
>
> --
> Shyno 

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 78

[Sana Saeed]

I am sending my message again because my mdp options were looking a little 
weird: 

hi 
I am performing protein ligand (pdb:4HBV)binding free energy calculations, I am 
done with complex simulation , now stuck in ligand simulation since last 2 
weeks. first i was getting zero energy, and when I changed some of parameters 
and position restraint my ligand , now i am getting LINCS warnings sometimes 
with NPT  and sometimes during production md. the strange part is that some of 
the lambdas are perfectly running while some of them crashes due to LINCS 
warnings, I know how to fix LINCS warnings (extending table size, decreasing 
step size, properly minimizing structure etc) but in  this case some of lambdas 
are running perfectly, which means the structure and parameters are fine. I 
decreased step size to 1 fs and got the same result, bow i decreased it to 
0.0001 ps. if someone ever got this kind of problem , please share your views. 
my second question is that the simple simulation for solvation free energy of 
small molecule and the ligand simulation in binding free energy system are 
same? i mean can i use the solvation free energy parameters from BEVAN lab's 
tutorial in this situation? in some of tutorials they use position restraints 
for ligand simulation in water, that is the reason I used the same. 
I provide npt and md.mdp parameters. if something is wrong kindly give 
comments. ignore the stepsize , I know its too small, I tried 0.001, 0.002, and 
this is the recent one, but couldn't see any difference. 
thanks in advance 

NPT.mdp 

define  =  -DPOSRES 
integrator  =  sd 
tinit   =  0 
dt  =  0.0001 
nsteps  =  50  ; 100 ps 
nstcomm =  100 

; Boundary conditions 
pbc =  xyz 

; Output 
nstxout =  0 
nstvout =  0 
nstfout =  0 
nstlog  =  100   ; 10 ps 
nstenergy   =  100   ; 10 ps 
nstcalcenergy   =  20 
nstxtcout   =  100   ; 10 ps 
xtc-precision   =  1000 
energygrps  =  System 

; Neighbour searching 
cutoff-scheme   = Verlet 
nstlist = 10  ; 20 fs 
ns-type = grid 
rlist   = 1.2   ; short-range neighborlist cutoff (in 
nm) 
rcoulomb= 1.2   ; short-range electrostatic cutoff (in 
nm) 
rvdw= 1.2   ; short-range van der Waals cutoff (in 
nm) 

; Constraints 
constraints =  none 
constraint-algorithm = lincs 
lincs_iter  = 1 ; accuracy of LINCS (1 is default) 
lincs_order = 12; also related to accuracy (4 is default) 
lincs-warnangle = 30; maximum angle that a bond can rotate before 
LINCS will complain 
^M 
; Electrostatics 
coulombtype = PME   ; Particle Mesh Ewald for long-range 
electrostatics 
pme-order   = 6 
fourierspacing  = 0.10  ; grid spacing for FFT 
ewald-rtol  = 1e-6  ; relative strength of the Ewald-shifted direct 
potential at rcoulomb 
optimize-fft= no 
ewald_geometry   = 3d 

; van der Waal's 
vdwtype=  Switch 
rvdw-switch =  0.9 
DispCorr=  EnerPres 

;Temperature Coupling (SD integrator => Langevin dynamics) 
tc_grps =  System 
tau_t   =  1.0 
ref_t   =  298.15 

; Pressure coupling 
Pcoupl  =  Berendsen 
pcoupltype  =  isotropic 
tau_p   =  2 
compressibility =  4.5e-05 
ref_p   =  1.0 

; Generate velocities 
gen_vel = yes 
gen_seed= -1 
gen_temp= 298.15 

continuation= no 

; Free energy control stuff = 
free-energy  = yes 
sc-alpha = 0.5 
sc-power = 1 
sc-sigma = 0.3 
init-lambda-state= 0 
coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 
1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 
1.0 
vdw-lambdas  = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 
0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 
1.0 
couple-moltype  = 15E 
couple-intramol = no 
couple-lambda0  = none 
couple-lambda1  = vdw-q 
nstdhdl  = 100 
calc-lambda-neighbors= -1 
refcoord-scaling = com 

PRODUCTION MD: 
md.mdp 

; Production MD 
; 
title   = production 

; Run parameters 
integrator  = sd; stochastic leap-frog integrator 
nsteps  = 250 
dt  = 0.0001 
nstcalcenergy   =  100 
energygrps  =  System 

; Periodic boundary conditions 
pbc = xyz   ; 3-D PBC 

; Output control 
nstvout = 500; save velocities to .trr file every 200 ps 
nstfout = 500; save forces to .trr file every 100 ps 
nstxout = 500   ; save coordinates every 5 

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[James Starlight]

 Is it better than
http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
 7  PArticularly for my case I need to convert from CG to FG the
structure of GPCR simulated within CG lipids excluding lipids in the
final FG model.

2016-03-17 15:49 GMT+01:00  :
> Hi James,
> There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to reconstruct 
> the atomistic structure from a CG structure.
> Here is the respective tutorial 
> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward
>  (from the MARTINI group), and here is the paper of the back mapping method:
> http://pubs.acs.org/doi/abs/10.1021/ct400617g
> Hope this helps.
> Best,
> Carlos
> --
>
> Carlos Navarro Retamal
> Ingeniero en Bioinformática
> Ph. D (c) en Ciencias Aplicadas.
> Centro de Bioinformática y Simulación Molecular
> Universidad de Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com o cnava...@utalca.cl
>
> On March 17, 2016 at 11:07:48 AM, James Starlight (jmsstarli...@gmail.com) 
> wrote:
>
> Dear Gromacs users!
>
> I wonder to ask for some suggestions about possibility of the CG to
> full atomistic conversion of sample pdb files extracted from the CG
> (Martini based) md trajectories. I will be especially thankful for any
> kind of the useful tutorial focused on the subject.
>
> Thanks for help in advance!
>
> J.
> --
> Gromacs Users mailing list
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Re: [gmx-users] Distance between two specific residues

[Justin Lemkul]

On 3/17/16 12:01 AM, Abid Channa wrote:

Dear Gromacs users, I am trying to calculate distance between two specific
residues of active site of my protein in MD. I have made separate .index file
of  two specific groups. Then I am trying this command " gmx distance -f
md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n index.ndx -tu ns ".
When I am selecting my residues numbers for option -select in above command.
error  appeared that pairs are not found in your selection residues (1st
residue "11 atoms" and 2nd residue "15 atoms" ). Kindly guide me how I
calculate distance between two specific residues in MD.


If your index groups are named, e.g. r_1 and r_2:

gmx distance gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg
-select 'com of group "r_1" plus com of group "r_2"' -n index.ndx -tu ns

-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] Volume and boundary Questions

[Tsjerk Wassenaar]

Hey :)

You can define any box 'shape', expressed in terms of the corresponding
lattice vectors, compliant with the rules stated in chapter 3 of the
manual. You can set a hexagonal prism cell using editconf, using the -box
and -angles options. In your case, the long edge should be along x, and has
90 degree angles with the other two vectors. It will end up something like
(fill in your own lengths)

gmx editconf -box 25 5 5 -angles 90 90 60

Hope it helps,

Tsjerk

On Fri, Mar 18, 2016 at 12:58 PM, Justin Lemkul  wrote:

>
>
> On 3/17/16 3:01 PM, ANAND AMITKUMAR DHARIA wrote:
>
>> Hello,
>>
>> I have two questions about setting up my box for simulation. Thank you for
>> any and all input in advance.
>>
>> 1. Is the simulation box dimensions and volume fixed throughout the
>> simulation (or are they allowed to fluctuate around the set dimensions)?
>>
>>
> That depends on the ensemble you choose for the simulation.  NVT = fixed
> box size.  NPT = the box size varies in response to pressure.
>
> 2. Is it possible to make custom box shapes (hexagonal) for a simulation
>> run instead of using the gromacs supported box types?
>>
>>
> If it's not supported, it's not supported.
>
> -Justin
>
> Context on my questions is that I would like to simulate proteins in
>> restrained nanotubes, where the tubes are the dimensions of the simulation
>> box (this way the entire system will look continuous with no space, when
>> periodic boundaries are applied).
>>
>> Please let me know if I need to clarify further.
>>
>> Thanks,
>> AD
>>
>>
> --
> ==
>
> 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] Hydrogen bonding pair selection

[Erik Marklund]

Dear Binwu,

Is there really a problem? With your selections you will not register any 
hbonds with N_H_ as the acceptor, since the other group contains no donors.

Kind regards,
Erik

> On 17 Mar 2016, at 20:10, Binwu Zhao  wrote:
> 
> Dear Gromacs Users,
> 
> I was trying to calculate the number of hydrogen bonds between the “O” on 
> Proline (acceptor) and the “N-H” on Glycine (donor) in my system. There are 
> 16 Proline residues and 32 Glycine residues. 
> 
> I first used command “make_ndx" to create two groups, PRO_&_O and N_H_,  
> corresponding to 16 “O” on Proline, and 32 “N-H” on Glycine, separately. Then 
> I tried to calculate the number of H-bonds between these two groups.
> 
> However, I encountered the following issue
> 
> Select a group: 15
> Selected 15: 'N_H_&_GLY'
> Select a group: 17
> Selected 17: 'PRO_&_O'
> Checking for overlap in atoms between N_H_&_GLY and PRO_&_O
> Calculating hydrogen bonds between N_H_&_GLY (64 atoms) and PRO_&_O (16 atoms)
> Found 32 donors and 48 acceptors
> 
> The “hbond” command is actually picking up the “N-H” on Glycine as acceptors 
> as well. May I ask if there is any way I can let just the “O” on Proline be 
> the acceptor and “N-H” on Glycine be the donor? In other words, I would like 
> to have 32 donors and 16 acceptors.
> 
> Is there any way to do that?
> 
> Thanks in advance!
> 
> Binwu
> 
> 
> 
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[gmx-users] Distance between two specific residues

[Abid Channa]

Dear Gromacs users,
I am trying to calculate distance between two specific residues of active site 
of my protein in MD. I have made separate .index file of  two specific groups. 
Then I am trying this command 
" gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select -n 
index.ndx -tu ns ". When I am selecting my residues numbers for option -select 
in above command. error  appeared that pairs are not found in your selection 
residues (1st residue "11 atoms" and 2nd residue "15 atoms" ). Kindly guide me 
how I calculate distance between two specific residues in MD.
Thanks,
Regards, 
Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
 Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
 International Center for Chemical and Biological Sciences  (ICCBS),
 University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. 
(309)
 Cell # +923013553051.
http://www.iccs.edu/


 

 
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[jkrieger]

You need to use a tool outside GROMACS to model in missing residues.
Discovery studio has capabilities to do this using MODELLER so you could
do that if you're comfortable with that software already (see
http://accelrys.com/services/training/life-science/protein-homology-modeling.html
which I just found through a Google search). I'm not sure what the issue
with the multiple of 11 is though.

Best wishes
James

> actually i m not getting how to proceed futher i m beginner to GROMACS
> it would be helpful if you can elaborate the process
>
> On 17 March 2016 at 21:54, Pradip Kaur  wrote:
>
>> so should i go for sol molecules :1612
>>  Na :11
>>
>> On 17 March 2016 at 21:44, Peter Stern 
>> wrote:
>>
>>> Missing atoms in GLU 474 is because the coordinates for the GLU side
>>> chain weren't resolved in the crystallographic data and aren't included
>>> in
>>> the pdb file.  Long bonds are probably because of missing residues.
>>> Check
>>> the pdb file for MISSING residues and atoms (listed in the header
>>> records).  Also, you can't just delete a residue and let Gromacs think
>>> that
>>> the preceding and following residues are connected (by an unphysical
>>> "long"
>>> bond).  The same goes for missing residues in the pdb file.
>>>
>>> I hope that the net charge was -5.999 otherwise, why add Na ions.  And
>>> as
>>> far as I know, 11*1612=17732.
>>>
>>> Peter Stern
>>>
>>> Sent from my iPad
>>>
>>> On 17 במרץ 2016, at 11:08, Pradip Kaur
>>> > kaur.pradip...@gmail.com>> wrote:
>>>
>>> i am currently working with 2bbo.pdb protein ,i have edited this
>>> protein
>>> in
>>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now i
>>> m
>>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
>>> running
>>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
>>> showing
>>>
>>> Warning: Long Bond (161-163 = 1.78456 nm)
>>>
>>> Warning: Long Bond (840-842 = 0.357037 nm)
>>>
>>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>>>
>>>
>>>
>>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
>>>
>>>
>>>
>>>
>>>
>>> ---
>>>
>>> Program pdb2gmx, VERSION 5.0.2
>>>
>>> Source code file:
>>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
>>> line:
>>> 1587
>>>
>>>
>>>
>>> Fatal error:
>>>
>>> There were 4 missing atoms in molecule Protein_chain_A, if you want to
>>> use
>>> this incomplete topology anyhow, use the option -missing
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>>
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>>
>>> *But  after ignoring missing atoms ,when i am running grompp command it
>>> shows that the system has non zero integral charge of 5.999.*
>>>
>>> *i have added command genion to neutalise the charge by adding 6 Na
>>> ions
>>> .After running the command it says that you have generated 17732
>>> solvent
>>> molecules which are not multiple of 11 .*
>>>
>>> *can any one help me with this problem*
>>> --
>>> Gromacs Users mailing list
>>>
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>>
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[gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Pradip Kaur]

i am currently working with 2bbo.pdb protein ,i have edited this protein in
Discovery studio 4.5 and deleted phenylalanine at 508 position , now i m
running molecular dynamics simulation  in GROMACS 5.0.2 bt after running
pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is showing

Warning: Long Bond (161-163 = 1.78456 nm)

Warning: Long Bond (840-842 = 0.357037 nm)

Warning: Long Bond (2237-2239 = 0.636287 nm)



WARNING: atom CG is missing in residue GLU 474 in the pdb file





WARNING: atom CD is missing in residue GLU 474 in the pdb file





WARNING: atom OE1 is missing in residue GLU 474 in the pdb file





WARNING: atom OE2 is missing in residue GLU 474 in the pdb file





---

Program pdb2gmx, VERSION 5.0.2

Source code file:
/build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1587



Fatal error:

There were 4 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology anyhow, use the option -missing

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors


*But  after ignoring missing atoms ,when i am running grompp command it
shows that the system has non zero integral charge of 5.999.*

*i have added command genion to neutalise the charge by adding 6 Na ions
.After running the command it says that you have generated 17732 solvent
molecules which are not multiple of 11 .*

*can any one help me with this problem*
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[gmx-users] Potential energy of each atom

[张正财]

Dear all,

  Could anyone tell me how can I output potential energy of each atom from 
a trajectory file?

  All the best,

 Zhengcai

Iggcas, CAS


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[gmx-users] Temperature dependence of virial of an initial configuration

[rakesh sharan]

Dear all, 

I have a question regarding computation of different components of virial of my 
starting initial configuration using Gromacs. When I am running job by setting 
nstep  = 0 (system is bulk spce water) to get potential energy and components 
of virial of my starting configuration, I am observing that output components 
of virial are strongly temperature dependent, even though potential energy is 
fixed. This is very surprising to me, as one would expect that both energy and 
virial of a starting configuration should be independent of temperature. I 
would highly appreciate any thought over this temperature dependent virial of 
my initial configuration. I would also appreciate very much if you could 
suggest any robust way to get the contribution of virial to the total pressure 
of a given configuration.

Thanks, 

Best, 
Rakesh
Sent from my iPad
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Pradip Kaur]

Thank you for all your suggestion ,ya I did some mistake after adding Na
ions   I selected system option (0)
As per your suggestion when I selected Sol (13) my problem solved ...Do I
need to go for modeller now or should I continue with this ...
On 18-Mar-2016 12:41 pm,  wrote:

> I'd suggest creating models with and without residue 508 in the target
> sequence. MODELLER should be able to rebuild the loop without residue 508
> and then you won't have long bonds. A hole in a protein is not physically
> or biologically meaningful. Rather a deletion mutation will end up in the
> ribosome inserting the next amino acid and linking it by a normal peptide
> bond.
>
> You'd then have to set up the system again from the model and I agree with
> Peter that you should check what you're doing against a tutorial to avoid
> the solvent error.
>
> Best wishes
> James
>
> > My project is on cystic fibrosis 508 del mutation ,what I m trying to do
> > is
> > that I have taken nuclear binding domain with 508phenylalanine (2bbo.pdb)
> > and I deleted that 508 phenylalanine to create a similar situation as
> what
> > occurs in body in case of cystic fibrosis ...after minimization of this
> > protein I ll dock the protein with a corrector ...and will see the
> binding
> > energy
> > On 18-Mar-2016 6:06 am, "Peter Stern" 
> wrote:
> >
> >> As James said, if you are using Discovery Studio it can model missing
> >> atoms and residues.  But why are you deleting a residue?  What do you
> >> hope
> >> to learn from this?  And don't just ignore missing atoms.
> >>
> >> I also don't understand the genion error, but I don't think you reported
> >> it exactly.  Didn't genion ask you to choose a solvent group and did you
> >> do
> >> that correctly?  I certainly didn't mean that you should choose 1612 sol
> >> molecules and 11 Na.  I simply meant that I didn't understand the error
> >> message since 17732 is divisible by 11.  I suspect that you didn't
> >> choose
> >> the correct group for solvent.
> >>
> >> Since you are a beginner may I suggest that you use one of the many
> >> Gromacs tutorials available choosing one appropriate to what you are
> >> trying
> >> to do?  I am sure that you can find these easily enough with Google.
> >>
> >> Best regards?
> >> Peter
> >>
> >> Sent from my iPhone
> >>
> >> > On 17 Mar 2016, at 12:27 PM, Pradip Kaur 
> >> wrote:
> >> >
> >> > actually i m not getting how to proceed futher i m beginner to GROMACS
> >> > it would be helpful if you can elaborate the process
> >> >
> >> >> On 17 March 2016 at 21:54, Pradip Kaur 
> >> wrote:
> >> >>
> >> >> so should i go for sol molecules :1612
> >> >> Na :11
> >> >>
> >> >>> On 17 March 2016 at 21:44, Peter Stern 
> >> wrote:
> >> >>>
> >> >>> Missing atoms in GLU 474 is because the coordinates for the GLU side
> >> >>> chain weren't resolved in the crystallographic data and aren't
> >> included in
> >> >>> the pdb file.  Long bonds are probably because of missing residues.
> >> Check
> >> >>> the pdb file for MISSING residues and atoms (listed in the header
> >> >>> records).  Also, you can't just delete a residue and let Gromacs
> >> think
> >> that
> >> >>> the preceding and following residues are connected (by an unphysical
> >> "long"
> >> >>> bond).  The same goes for missing residues in the pdb file.
> >> >>>
> >> >>> I hope that the net charge was -5.999 otherwise, why add Na ions.
> >> And
> >> as
> >> >>> far as I know, 11*1612=17732.
> >> >>>
> >> >>> Peter Stern
> >> >>>
> >> >>> Sent from my iPad
> >> >>>
> >> >>> On 17 במרץ 2016, at 11:08, Pradip Kaur  >>  >> >>> kaur.pradip...@gmail.com>> wrote:
> >> >>>
> >> >>> i am currently working with 2bbo.pdb protein ,i have edited this
> >> protein
> >> >>> in
> >> >>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now
> >> i
> >> m
> >> >>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
> >> running
> >> >>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
> >> >>> showing
> >> >>>
> >> >>> Warning: Long Bond (161-163 = 1.78456 nm)
> >> >>>
> >> >>> Warning: Long Bond (840-842 = 0.357037 nm)
> >> >>>
> >> >>> Warning: Long Bond (2237-2239 = 0.636287 nm)
> >> >>>
> >> >>>
> >> >>>
> >> >>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>>
> >> >>> ---
> >> >>>
> >> >>> Program pdb2gmx, VERSION 5.0.2
> >> >>>

[gmx-users] About The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

[Poncho Arvayo Zatarain]

Hello, due to one of my last question and about the error:  The cut-off length 
is longer than half the shortest box vector or longer than the smallest box 
diagonal element. Increase the box size or decrease rlist. How can do large the 
box? My .gro files vectors are 8.9 8.90 and 7.90 and my cutoff 
lenghts are: nstlist = 10 ; 10 fsrlist= 1.2 ; short-range neighborlist 
cutoff (in nm)rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)rvdw = 
1.2 ; short-range van der Waals cutoff (in nm)vdwtype = cutoff
  
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Re: [gmx-users] Potential energy of each atom

[张正财]

> Subject: Re: [gmx-users] Potential energy of each atom
> Message-ID: <56eba4a9.8020...@xray.bmc.uu.se>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> On 18/03/16 03:40, ??? wrote:
> > Dear all,
> >
> >Could anyone tell me how can I output potential energy of each atom 
> > from a trajectory file?
> >
> What does that mean?

Like the command in LAMMPS, "compute pe/atom", I want to display the potential 
energy of each atom in simulation system. is it possible in gromacs?
> 
> If you have a Na+ and a Cl- in the gas phase Gromacs can compute Coulomb 
> energy and Lennard Jones energy. But how would you partition that over 
> atoms?
> 
> 
> 
> >All the best,
> >
> >   Zhengcai
> >
> >  Iggcas, CAS
> >
> >
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> 
> 



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Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[James Starlight]

what I have found from the
./initram.sh -h

-f   Input coarse grained structure
   *FILE:  None
-p   Input atomistic target topology
   *FILE:  None


does it means that -p should be full atomic topology of the system
(not coarse grained) ? Is so whether is possible to make such CG to FG
conversion having only CG input data

2016-03-17 17:04 GMT+01:00 James Starlight :
> Just tested the ./initram.sh script embedded within the
>
> Unfortunatelly for my case It didnt works
>
> 1- I firstly extract the gro file consisted of the protein CG
> representation only from my Cg.gro using below command and selecting
> protein group
> g_editconf -f system.gro -n -o protein.gro
>
> than I edit my topology putting here only protein itp
>
> #include "./params/martini_v2.1.itp"
> #include "./params/D2.itp"
>
> [ system ]
> Single Low D2
>
> [ molecules ]
> D2   1
>
>
> finally than I apply script on those two files
> ./initram.sh -f protein.gro -o aa_charmm.gro -to charmm36 -p protein.top
>
>
> obtaining error
>
> ---
> Program g_grompp, VERSION 4.5.7
> Source code file:
> /builddir/build/BUILD/gromacs-4.5.7/src/kernel/grompp.c, line: 523
>
> Fatal error:
> number of coordinates in coordinate file (0-backward.gro, 0)
>  does not match topology (backmapped.top, 598)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> 2016-03-17 16:24 GMT+01:00 James Starlight :
>>  Is it better than
>> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
>>  7  PArticularly for my case I need to convert from CG to FG the
>> structure of GPCR simulated within CG lipids excluding lipids in the
>> final FG model.
>>
>> 2016-03-17 15:49 GMT+01:00  :
>>> Hi James,
>>> There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to 
>>> reconstruct the atomistic structure from a CG structure.
>>> Here is the respective tutorial 
>>> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward
>>>  (from the MARTINI group), and here is the paper of the back mapping method:
>>> http://pubs.acs.org/doi/abs/10.1021/ct400617g
>>> Hope this helps.
>>> Best,
>>> Carlos
>>> --
>>>
>>> Carlos Navarro Retamal
>>> Ingeniero en Bioinformática
>>> Ph. D (c) en Ciencias Aplicadas.
>>> Centro de Bioinformática y Simulación Molecular
>>> Universidad de Talca
>>> Av. Lircay S/N, Talca, Chile
>>> T: (+56) 712201 798
>>> E: carlos.navarr...@gmail.com o cnava...@utalca.cl
>>>
>>> On March 17, 2016 at 11:07:48 AM, James Starlight (jmsstarli...@gmail.com) 
>>> wrote:
>>>
>>> Dear Gromacs users!
>>>
>>> I wonder to ask for some suggestions about possibility of the CG to
>>> full atomistic conversion of sample pdb files extracted from the CG
>>> (Martini based) md trajectories. I will be especially thankful for any
>>> kind of the useful tutorial focused on the subject.
>>>
>>> Thanks for help in advance!
>>>
>>> J.
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at 
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Pradip Kaur]

My project is on cystic fibrosis 508 del mutation ,what I m trying to do is
that I have taken nuclear binding domain with 508phenylalanine (2bbo.pdb)
and I deleted that 508 phenylalanine to create a similar situation as what
occurs in body in case of cystic fibrosis ...after minimization of this
protein I ll dock the protein with a corrector ...and will see the binding
energy
On 18-Mar-2016 6:06 am, "Peter Stern"  wrote:

> As James said, if you are using Discovery Studio it can model missing
> atoms and residues.  But why are you deleting a residue?  What do you hope
> to learn from this?  And don't just ignore missing atoms.
>
> I also don't understand the genion error, but I don't think you reported
> it exactly.  Didn't genion ask you to choose a solvent group and did you do
> that correctly?  I certainly didn't mean that you should choose 1612 sol
> molecules and 11 Na.  I simply meant that I didn't understand the error
> message since 17732 is divisible by 11.  I suspect that you didn't choose
> the correct group for solvent.
>
> Since you are a beginner may I suggest that you use one of the many
> Gromacs tutorials available choosing one appropriate to what you are trying
> to do?  I am sure that you can find these easily enough with Google.
>
> Best regards?
> Peter
>
> Sent from my iPhone
>
> > On 17 Mar 2016, at 12:27 PM, Pradip Kaur 
> wrote:
> >
> > actually i m not getting how to proceed futher i m beginner to GROMACS
> > it would be helpful if you can elaborate the process
> >
> >> On 17 March 2016 at 21:54, Pradip Kaur 
> wrote:
> >>
> >> so should i go for sol molecules :1612
> >> Na :11
> >>
> >>> On 17 March 2016 at 21:44, Peter Stern 
> wrote:
> >>>
> >>> Missing atoms in GLU 474 is because the coordinates for the GLU side
> >>> chain weren't resolved in the crystallographic data and aren't
> included in
> >>> the pdb file.  Long bonds are probably because of missing residues.
> Check
> >>> the pdb file for MISSING residues and atoms (listed in the header
> >>> records).  Also, you can't just delete a residue and let Gromacs think
> that
> >>> the preceding and following residues are connected (by an unphysical
> "long"
> >>> bond).  The same goes for missing residues in the pdb file.
> >>>
> >>> I hope that the net charge was -5.999 otherwise, why add Na ions.  And
> as
> >>> far as I know, 11*1612=17732.
> >>>
> >>> Peter Stern
> >>>
> >>> Sent from my iPad
> >>>
> >>> On 17 במרץ 2016, at 11:08, Pradip Kaur   >>> kaur.pradip...@gmail.com>> wrote:
> >>>
> >>> i am currently working with 2bbo.pdb protein ,i have edited this
> protein
> >>> in
> >>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now i
> m
> >>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
> running
> >>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
> >>> showing
> >>>
> >>> Warning: Long Bond (161-163 = 1.78456 nm)
> >>>
> >>> Warning: Long Bond (840-842 = 0.357037 nm)
> >>>
> >>> Warning: Long Bond (2237-2239 = 0.636287 nm)
> >>>
> >>>
> >>>
> >>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> ---
> >>>
> >>> Program pdb2gmx, VERSION 5.0.2
> >>>
> >>> Source code file:
> >>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
> line:
> >>> 1587
> >>>
> >>>
> >>>
> >>> Fatal error:
> >>>
> >>> There were 4 missing atoms in molecule Protein_chain_A, if you want to
> use
> >>> this incomplete topology anyhow, use the option -missing
> >>>
> >>> For more information and tips for troubleshooting, please check the
> >>> GROMACS
> >>>
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>>
> >>>
> >>> *But  after ignoring missing atoms ,when i am running grompp command it
> >>> shows that the system has non zero integral charge of 5.999.*
> >>>
> >>> *i have added command genion to neutalise the charge by adding 6 Na
> ions
> >>> .After running the command it says that you have generated 17732
> solvent
> >>> molecules which are not multiple of 11 .*
> >>>
> >>> *can any one help me with this problem*
> >>> --
> >>> 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 

Re: [gmx-users] Using FFTK generated parameter file for Protein-Ligand simulations

[Justin Lemkul]

On 3/16/16 10:18 PM, Soumya Lipsa Rath wrote:

Dear Gromacs Users,

I have to run a protein-ligand system. I am using CHARMM36 ff for the
simulation. For generating the parameters for the ligand molecule I used
the forcefield development toolkit of vmd, which gives CHARMM compatible
parameters.

But, I am unable to understand how should I include the parameters I had
obtained. I went through the tutorial files which shows an example of
PRODRG server for generating the itp file, but my ligand contains metal
atoms. I would appreciate if somebody could suggest me how to solve this.



What are the ligands?  What metal?

Don't use PRODRG; it's only intended for GROMOS force fields (and even then, the 
topologies need a lot of work).


-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

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http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] simulation a box of water

[Justin Lemkul]

On 3/16/16 8:30 AM, Saeed Nasiri wrote:

Dear all

I want to simulate a box of water (2*2*2 nm with 1401 molecules). Is there
difference between using a model for water molecules and importing this
molecule from other programs(such as nwchem)?
I want to do a small simulation and it is not important to treat water
molecules explicitly.
I used a water.pdb file to generate the box with this command:



I'm confused.  You don't need to treat water explicitly, but you're building a 
box of explicit water molecules?  Can you please explain in greater detail what 
you're trying to accomplish?  If you have a custom set of water parameters, you 
need to introduce these yourself in suitable GROMACS format.


pdb2gmx generates topologies.  By executing it in the manner below, you are 
essentially telling pdb2gmx "I have water, but don't write a topology for water" 
so pdb2gmx correctly fails.


-Justin



*gmx_mpi insert-molecules -ci WATER.pdb -nmol 3000 -box 2 2 2 -o
water_box.gro*
  ...
  
Added 467 molecules (out of 3000 requested)
Writing generated configuration to water_box.gro

Output configuration contains 1401 atoms in 934 residues

gcq#247: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix"
(Indeep)

after that I want to create topol.gro file, but I got an error ?


*gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh*
   :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

 GROMACS is written by:
  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
Bjelkmar
  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
Kutzner
 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
and the project leaders:
 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx_mpi
Data prefix:  /usr/local/gromacs
Command line:
   gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh


Select the Force Field:
 From '/usr/local/gromacs/share/gromacs/top':
  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
1999-2012, 2003)
  2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
  3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
461-469, 1996)
  4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
1049-1074, 2000)
  5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
712-725, 2006)
  6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
Proteins 78, 1950-58, 2010)
  7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
  9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat

Select the Water Model:
  1: TIP4P  TIP 4-point, recommended
  2: TIP4PEW TIP 4-point with Ewald
  3: TIP3P  TIP 3-point
  4: TIP5P  TIP 5-point (see http://redmine.gromacs.org/issues/1348 for
issues)
  5: TIP5P  TIP 5-point improved for Ewald sums
  6: SPCsimple point charge
  7: SPC/E  extended simple point charge
  8: None
8
Opening force field file
/usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading water_box.gro...
Read 'UNNAMED', 467 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 0 chains and 1 blocks of water and 934 residues with 467 atoms

   chain  #res #atoms
   1 ' '   933467  (only water)

No occupancies in water_box.gro
Opening force field file

Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[Justin Lemkul]

On 3/18/16 6:31 AM, jkrie...@mrc-lmb.cam.ac.uk wrote:

Definitely use modeller first. Then go through everything again.

I'm happy you solved the problem with the multiple of 11. Perhaps Justin
or Mark or someone could comment on why it said that. While it makes sense
to replace solvent atoms with ions in most cases, I would have thought any
replacement would work including parts of proteins and ligands.



When adding ions, genion assumes the user is replacing a block of uniform 
molecules.  So it checks the first residue in the selected group, and if it 
doesn't match the subsequent residues, it fails.  So if one chooses something 
like the protein or the whole system, the number of atoms in each residue will 
not be the same.  So clearly the user has done something very wrong.


-Justin


Best wishes
James


Thank you for all your suggestion ,ya I did some mistake after adding Na
ions   I selected system option (0)
As per your suggestion when I selected Sol (13) my problem solved ...Do I
need to go for modeller now or should I continue with this ...
On 18-Mar-2016 12:41 pm,  wrote:


I'd suggest creating models with and without residue 508 in the target
sequence. MODELLER should be able to rebuild the loop without residue
508
and then you won't have long bonds. A hole in a protein is not
physically
or biologically meaningful. Rather a deletion mutation will end up in
the
ribosome inserting the next amino acid and linking it by a normal
peptide
bond.

You'd then have to set up the system again from the model and I agree
with
Peter that you should check what you're doing against a tutorial to
avoid
the solvent error.

Best wishes
James


My project is on cystic fibrosis 508 del mutation ,what I m trying to

do

is
that I have taken nuclear binding domain with 508phenylalanine

(2bbo.pdb)

and I deleted that 508 phenylalanine to create a similar situation as

what

occurs in body in case of cystic fibrosis ...after minimization of

this

protein I ll dock the protein with a corrector ...and will see the

binding

energy
On 18-Mar-2016 6:06 am, "Peter Stern" 

wrote:



As James said, if you are using Discovery Studio it can model missing
atoms and residues.  But why are you deleting a residue?  What do you
hope
to learn from this?  And don't just ignore missing atoms.

I also don't understand the genion error, but I don't think you

reported

it exactly.  Didn't genion ask you to choose a solvent group and did

you

do
that correctly?  I certainly didn't mean that you should choose 1612

sol

molecules and 11 Na.  I simply meant that I didn't understand the

error

message since 17732 is divisible by 11.  I suspect that you didn't
choose
the correct group for solvent.

Since you are a beginner may I suggest that you use one of the many
Gromacs tutorials available choosing one appropriate to what you are
trying
to do?  I am sure that you can find these easily enough with Google.

Best regards?
Peter

Sent from my iPhone


On 17 Mar 2016, at 12:27 PM, Pradip Kaur 

wrote:


actually i m not getting how to proceed futher i m beginner to

GROMACS

it would be helpful if you can elaborate the process


On 17 March 2016 at 21:54, Pradip Kaur 

wrote:


so should i go for sol molecules :1612
 Na :11


On 17 March 2016 at 21:44, Peter Stern



wrote:


Missing atoms in GLU 474 is because the coordinates for the GLU

side

chain weren't resolved in the crystallographic data and aren't

included in

the pdb file.  Long bonds are probably because of missing

residues.

Check

the pdb file for MISSING residues and atoms (listed in the header
records).  Also, you can't just delete a residue and let Gromacs

think
that

the preceding and following residues are connected (by an

unphysical

"long"

bond).  The same goes for missing residues in the pdb file.

I hope that the net charge was -5.999 otherwise, why add Na ions.

And
as

far as I know, 11*1612=17732.

Peter Stern

Sent from my iPad

On 17 במרץ 2016, at 11:08, Pradip Kaur

> wrote:

i am currently working with 2bbo.pdb protein ,i have edited this

protein

in
Discovery studio 4.5 and deleted phenylalanine at 508 position ,

now

i
m

running molecular dynamics simulation  in GROMACS 5.0.2 bt after

running

pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it

is

showing

Warning: Long Bond (161-163 = 1.78456 nm)

Warning: Long Bond (840-842 = 0.357037 nm)

Warning: Long Bond (2237-2239 = 0.636287 nm)



WARNING: atom CG is missing in residue GLU 474 in the pdb file





WARNING: atom CD is missing in residue GLU 474 in the pdb file





WARNING: atom OE1 is missing in residue GLU 474 in the pdb file





WARNING: atom OE2 is missing in residue GLU 474 in the pdb file





---

Re: [gmx-users] Potential energy of each atom

[David van der Spoel]

On 18/03/16 03:40, 张正财 wrote:

Dear all,

   Could anyone tell me how can I output potential energy of each atom from 
a trajectory file?


What does that mean?

If you have a Na+ and a Cl- in the gas phase Gromacs can compute Coulomb 
energy and Lennard Jones energy. But how would you partition that over 
atoms?





   All the best,

  Zhengcai

 Iggcas, CAS





--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] simulation a box of water

[Saeed Nasiri]

thanks so much for all the comments.

as far as I know the water molecules created by models have solid bods and
angles. I want to extract thermodynamical parameters from the simulation,
for this purpose I used this method.
Is this a trick to used water molecule explicitly?
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Re: [gmx-users] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

[Justin Lemkul]

On 3/15/16 12:23 PM, Poncho Arvayo Zatarain wrote:

Hello, i ḿ working in a lipid bilayer using charmm36 forcefield and trying to
do NVT equilibration but when i use grompp for nvt i receive the folowing
error:  The cut-off length is longer than half the shortest box vector or
longer than the smallest box diagonal element. Increase the box size or
decrease rlist. I read about this at Manual of Gromacs and decrease the rlist
but the error is still there. The other solution is to increase the box size
but, it is safe to do this? or what can i do? i can attach my nvt.mdp file if
you wantThanks



Cutoffs are an intrinsic part of the force field, so your box must be large 
enough to avoid minimum image violations.  Any reasonable lipid bilayer should 
be in a box large enough that no issues should arise.


-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] Custom forcefield tutorial?

[Justin Lemkul]

On 3/18/16 6:30 AM, Michał Kadlof wrote:

Hello,

I would like to perform some simulations with my own simple forcefield.
Just a chain of beads, with Lenard-Jones, some harmonic and angle potential, 
and play with it's parameters.
I don't want to write all the computing part from the scratch. I rather to use 
Gromacs (if it is possible?), especially that MPI and GPU support is expected 
here.

I didn't find any suitable documentation or tutorial for this purposes.

Can you help me with this issue or give some advice?



Chapter 5 of the manual describes the force field format.  If you're only 
dealing with LJ, bonds, and angles, it should be quite straightforward to write 
the force field files.


-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] umberlla sampling

[Justin Lemkul]

On 3/18/16 5:21 AM, Ali Mohyeddin wrote:

Dear Justin,

In the tutorial of "umbrella sampling
",
what happens if we set the pull_coord1_rate to zero value? Does it work
like a harmonic force (spring) between two groups with a constant distance
averagely?  Indeed, I need to fix the distance between two groups and then
start to pull them.



That's exactly what it does.

-Justin


;Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 1
pull_group1_name= Chain_B
pull_group2_name= Chain_A
pull_coord1_type= umbrella  ; harmonic biasing force
pull_coord1_geometry= distance  ; simple distance increase
pull_coord1_groups  = 1 2
pull_coord1_dim = N N Ypull_coord1_rate= 0
; 0 nm per ps = 10 nm per ns
pull_coord1_k   = 1000  ; kJ mol^-1 nm^-2
pull_coor1_start= yes   ; define initial COM distance >0

Best regards,

Ali Mohyeddin



--
==

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] Building dimer system using MARTINI

[James Starlight]

Dear Gromacs Users!

I wonder to ask suggestions regarding assembly of the oligomeric
systems parametrized using martini ff.

Briefly using only 1 type of protein the situation is very simple - 1)
prepare box for the monomer using martinize, 2) equilibrate it and 3)
make replicas vwithin one system using genconf.

however what I should to do if I dealing with the simulation of 2
different proteins ? E.g is it possible to make initial system using
martinize for 2 different proteins within one system or I should
alrernatively make 2 different systems and after equilibration join
them together? How it could be achived for the oligomeric membrane
protein system assuming that I want to start simulation for 2 unbound
receptors within 1 membrane and simulate its assosiation ?

Thanks for help!!

J.
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[jkrieger]

Definitely use modeller first. Then go through everything again.

I'm happy you solved the problem with the multiple of 11. Perhaps Justin
or Mark or someone could comment on why it said that. While it makes sense
to replace solvent atoms with ions in most cases, I would have thought any
replacement would work including parts of proteins and ligands.

Best wishes
James

> Thank you for all your suggestion ,ya I did some mistake after adding Na
> ions   I selected system option (0)
> As per your suggestion when I selected Sol (13) my problem solved ...Do I
> need to go for modeller now or should I continue with this ...
> On 18-Mar-2016 12:41 pm,  wrote:
>
>> I'd suggest creating models with and without residue 508 in the target
>> sequence. MODELLER should be able to rebuild the loop without residue
>> 508
>> and then you won't have long bonds. A hole in a protein is not
>> physically
>> or biologically meaningful. Rather a deletion mutation will end up in
>> the
>> ribosome inserting the next amino acid and linking it by a normal
>> peptide
>> bond.
>>
>> You'd then have to set up the system again from the model and I agree
>> with
>> Peter that you should check what you're doing against a tutorial to
>> avoid
>> the solvent error.
>>
>> Best wishes
>> James
>>
>> > My project is on cystic fibrosis 508 del mutation ,what I m trying to
>> do
>> > is
>> > that I have taken nuclear binding domain with 508phenylalanine
>> (2bbo.pdb)
>> > and I deleted that 508 phenylalanine to create a similar situation as
>> what
>> > occurs in body in case of cystic fibrosis ...after minimization of
>> this
>> > protein I ll dock the protein with a corrector ...and will see the
>> binding
>> > energy
>> > On 18-Mar-2016 6:06 am, "Peter Stern" 
>> wrote:
>> >
>> >> As James said, if you are using Discovery Studio it can model missing
>> >> atoms and residues.  But why are you deleting a residue?  What do you
>> >> hope
>> >> to learn from this?  And don't just ignore missing atoms.
>> >>
>> >> I also don't understand the genion error, but I don't think you
>> reported
>> >> it exactly.  Didn't genion ask you to choose a solvent group and did
>> you
>> >> do
>> >> that correctly?  I certainly didn't mean that you should choose 1612
>> sol
>> >> molecules and 11 Na.  I simply meant that I didn't understand the
>> error
>> >> message since 17732 is divisible by 11.  I suspect that you didn't
>> >> choose
>> >> the correct group for solvent.
>> >>
>> >> Since you are a beginner may I suggest that you use one of the many
>> >> Gromacs tutorials available choosing one appropriate to what you are
>> >> trying
>> >> to do?  I am sure that you can find these easily enough with Google.
>> >>
>> >> Best regards?
>> >> Peter
>> >>
>> >> Sent from my iPhone
>> >>
>> >> > On 17 Mar 2016, at 12:27 PM, Pradip Kaur 
>> >> wrote:
>> >> >
>> >> > actually i m not getting how to proceed futher i m beginner to
>> GROMACS
>> >> > it would be helpful if you can elaborate the process
>> >> >
>> >> >> On 17 March 2016 at 21:54, Pradip Kaur 
>> >> wrote:
>> >> >>
>> >> >> so should i go for sol molecules :1612
>> >> >> Na :11
>> >> >>
>> >> >>> On 17 March 2016 at 21:44, Peter Stern
>> 
>> >> wrote:
>> >> >>>
>> >> >>> Missing atoms in GLU 474 is because the coordinates for the GLU
>> side
>> >> >>> chain weren't resolved in the crystallographic data and aren't
>> >> included in
>> >> >>> the pdb file.  Long bonds are probably because of missing
>> residues.
>> >> Check
>> >> >>> the pdb file for MISSING residues and atoms (listed in the header
>> >> >>> records).  Also, you can't just delete a residue and let Gromacs
>> >> think
>> >> that
>> >> >>> the preceding and following residues are connected (by an
>> unphysical
>> >> "long"
>> >> >>> bond).  The same goes for missing residues in the pdb file.
>> >> >>>
>> >> >>> I hope that the net charge was -5.999 otherwise, why add Na ions.
>> >> And
>> >> as
>> >> >>> far as I know, 11*1612=17732.
>> >> >>>
>> >> >>> Peter Stern
>> >> >>>
>> >> >>> Sent from my iPad
>> >> >>>
>> >> >>> On 17 במרץ 2016, at 11:08, Pradip Kaur
>> > >> > >> >>> kaur.pradip...@gmail.com>> wrote:
>> >> >>>
>> >> >>> i am currently working with 2bbo.pdb protein ,i have edited this
>> >> protein
>> >> >>> in
>> >> >>> Discovery studio 4.5 and deleted phenylalanine at 508 position ,
>> now
>> >> i
>> >> m
>> >> >>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
>> >> running
>> >> >>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it
>> is
>> >> >>> showing
>> >> >>>
>> >> >>> Warning: Long Bond (161-163 = 1.78456 nm)
>> >> >>>
>> >> >>> Warning: Long Bond (840-842 = 0.357037 nm)
>> >> >>>
>> >> >>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> WARNING: atom CG is 

Re: [gmx-users] creating representative structures

[Tsjerk Wassenaar]

Hi Stephane,

The difference is too large for rounding errors. I was not suggesting
different selections, but rather mass-weighting versus non-mass-weighting.

Cheers,

Tsjerk
On Mar 17, 2016 23:15, "Téletchéa Stéphane" <
stephane.teletc...@univ-nantes.fr> wrote:

> Le 16/03/2016 16:54, Shyno Mathew a écrit :
>
>> I wrote a tcl script to do cluster analysis, using gromos method. My
>> results are slightly different from the g_cluster results. I see the
>> difference is coming from RMSD values. For example, with g_cluster, “The
>> RMSD ranges from 0.149614 to 0.220387 nm”
>>
>>
>> However with the tcl script, and after converting RMSD from Å to nm, the
>> value ranges from 0.173347 to 0.234409 nm! I am using the same selection
>> in
>> both cases for RMSD calculations.
>>
>
> Dear Shyno,
>
> As Tserk mentioned earlier you may have different selections, but
> be very careful when you compare floating point numbers especially
> in interpreted languages, since most of the time their precision is not
> very "reliable".
> See the discussions in http://wiki.tcl.tk/11969 and http://wiki.tcl.tk/879
> for instance...
>
> Either way you have to test :-)
>
> Best,
>
> Stéphane
>
> --
> Team Protein Design In Silico
> UFIP, UMR 6286 CNRS, UFR Sciences et Techniques,
> 2, rue de la Houssinière, Bât. 25, Nantes cedex 03, France
> Tél : +33 251 125 636 - Fax : +33 251 125 632
> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
>
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Re: [gmx-users] Questions about parameters

[abhishek khetan]

Dear Justin,

Thanks for your insightful replies. I decided that I will not use position
restraints but rather all-bond constraints because I want to allow the
molecules to move freely and reorient without getting disintegrated,
although they did not look like disintegrating even without constraints.
Distance restraints might be an even better option in this regard but I
have to understand it better. Therefore, I have still some more questions
as I am totally new to MD and gromacs. They are as follows:

> 1a. Is it okay (in sense of physical accuracy) to change the tcoupl and
integrator when going from NVT to NPT? -- Without knowing what errors you
were getting, it's hard to say.  Just about all combinations should be
supported so I don't know why this is necessary.  But in  any case, any
time you change an algorithm, you need to allow sufficient time for
relaxation.
==> I am allowing for 1000 ps NVT followed by 1000 ps of NPT, which seems
okay enough for relaxation. When I use integrator = md, then I cannot use
tcoupl = nose-hoover. When I use integrator = md-vv with tcoupl =
nose-hoover, I cannot use pcoupl = MTTK because it gives the error - "MTTK
not compatible with lincs -- use shake instead." and "Constraints are not
implemented with MTTK pressure control". So I cannot use MTTK with
constraints. As, I explained, I want to allow movement of molecules without
disintegrating them, therefore I want to use constraints instead of
absolute position restraints. Then, the only option I am left with is to
use pcoupl = parrinello-rahman, for which I cannot use integrator = md-vv,
which means I cannot use tcoupl = nose-hoover and therefore I have to use
tcoupl = v-rescale, which is the closest thing to nose-hoover. Seen this
way, most (desirable and physically accurate) combinations are not
possible.

> 2.d The volume after NPT with no constraints was 2.20x2.20x2.20 nm3 and
the volume after NPT with contraints = all bonds was 2.22x2.22x2.22 nm3.
They are so close to the original, which should I trust more in terms of
physical reality (essentially same as question 2a.)? -- The volume of a
single snapshot means nothing.  The ensemble average is probably
indistinguishable, but that's what you should check.  Such a tiny box is
going  to be prone to massive pressure fluctuations, though, so anything
related to  pressure or density is probably unreliable, especially with
Parrinello-Rahman.
==> You're spot on. The pressure fluctuations are massive(-200 to 800
bars). But then, can it not find its equilibrium volume because of the
pressure coupling I used ? Is increasing the box size with several more
molecules the only way to achieve reasonable pressure and density
fluctuations? Could you please guide me to the page/tutorial/link where I
can learn more about the ensemble average and look at all the samples. Is
there a theory article on this ?

> 3a. What is way position restraints work? I understand that they
introduce a heavy energy penalty on the movement of atoms, but do they
apply this penalty on the absolute deviation of the atoms' positions or on
the deviation of the atom's positions with respect to the centre of mass of
the respective molecule? -- Depends on the what option you choose for
refcoord_scaling.
> 4a. How does the refcoord_scaling work? when i use 'com', does it mean
that the coordinate are scaled with respect to the COM of the whole system
in a way that even bond lengths within the individual molecules change ? --
This is explained in the manual.
==> The gromacs manual 5.1.2 doesn't not have the string 'refcoord' or
'refcoord_scaling'. When I look up the mdp options online, then it says
'refcoord_scaling = com'
would  "Scale the center of mass of the reference coordinates with the
scaling matrix of the pressure coupling. The vectors of each reference
coordinate to the center of mass are not scaled. Only one COM is used, even
when there are multiple molecules with position restraints". My question is
- whats the meaning of reference coordinates? to what 'reference' are these
coordinates referenced ? How are they different from the absolute
coordinates ? In case I understand it correctly, these are the coordinates
referenced to the COM of the entire system and this kind of
refcoord_scaling doesn't change the bond lengths but just moves the COMs of
the - which to me is also what I want. However, if I use 'refcoord_scaling
= all', does this mean the bond lengths will also change ? When I use
'refcoord_scaling=com' along with position restraints, does it mean that
the molecule's COM are scaled freely but the internal positions are
restrained with heavy energy penalty? - This would be ideal and awesome,
because right now I am using constraints instead of restraints. The manual
doesn't define these terms clearly, therefore, it would be very kind if you
could please clarify this.

Last question: The last set of lines from the *log from my NPT simulation
were:

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[James Starlight]

Just tested the ./initram.sh script embedded within the

Unfortunatelly for my case It didnt works

1- I firstly extract the gro file consisted of the protein CG
representation only from my Cg.gro using below command and selecting
protein group
g_editconf -f system.gro -n -o protein.gro

than I edit my topology putting here only protein itp

#include "./params/martini_v2.1.itp"
#include "./params/D2.itp"

[ system ]
Single Low D2

[ molecules ]
D2   1


finally than I apply script on those two files
./initram.sh -f protein.gro -o aa_charmm.gro -to charmm36 -p protein.top


obtaining error

---
Program g_grompp, VERSION 4.5.7
Source code file:
/builddir/build/BUILD/gromacs-4.5.7/src/kernel/grompp.c, line: 523

Fatal error:
number of coordinates in coordinate file (0-backward.gro, 0)
 does not match topology (backmapped.top, 598)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

2016-03-17 16:24 GMT+01:00 James Starlight :
>  Is it better than
> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
>  7  PArticularly for my case I need to convert from CG to FG the
> structure of GPCR simulated within CG lipids excluding lipids in the
> final FG model.
>
> 2016-03-17 15:49 GMT+01:00  :
>> Hi James,
>> There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to reconstruct 
>> the atomistic structure from a CG structure.
>> Here is the respective tutorial 
>> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward
>>  (from the MARTINI group), and here is the paper of the back mapping method:
>> http://pubs.acs.org/doi/abs/10.1021/ct400617g
>> Hope this helps.
>> Best,
>> Carlos
>> --
>>
>> Carlos Navarro Retamal
>> Ingeniero en Bioinformática
>> Ph. D (c) en Ciencias Aplicadas.
>> Centro de Bioinformática y Simulación Molecular
>> Universidad de Talca
>> Av. Lircay S/N, Talca, Chile
>> T: (+56) 712201 798
>> E: carlos.navarr...@gmail.com o cnava...@utalca.cl
>>
>> On March 17, 2016 at 11:07:48 AM, James Starlight (jmsstarli...@gmail.com) 
>> wrote:
>>
>> Dear Gromacs users!
>>
>> I wonder to ask for some suggestions about possibility of the CG to
>> full atomistic conversion of sample pdb files extracted from the CG
>> (Martini based) md trajectories. I will be especially thankful for any
>> kind of the useful tutorial focused on the subject.
>>
>> Thanks for help in advance!
>>
>> J.
>> --
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[gmx-users] Thermostatting in non-equilibrium dynamics

[Ondrej Kroutil]

Dear all,

The question I have has been posted here by other user last year but with
not satisfactory answer (if I have searched properly!), so I'd like to open
this topic again.
It concerns non-equilibrium dynamics and thermostating. For simulations of
Poisseuille flow in explicit atomistic slabs we need to exclude certain
dimensions (direction of the applied external force, possibly also the
direction perpendicular to the slab) from calculation of kinetic energy for
thermostatting (absolutely important) as well as to turn on/off
thermostatting of rotational degrees of freedom (not so critical).

We see that some exclusion of the streaming velocities is implemented in
viscosity calculations, but we’d need to make it more general. In the same
way as one can specify pbc in xyz or xy, we’d love to be able to set
thermostatting of xyz velocities or xy only or x only. This is essential
for us to be able to use Gromacs for our non-equilibrium simulations.

We used the above thermostatting using our own code in publications:

M. Předota, P. T. Cummings, and D. J. Wesolowski: “Electric Double Layer at
the Rutile (110) Surface. 3. Inhomogeneous Viscosity and Diffusivity
Measurement by Computer Simulations” J. Phys. Chem. C
111, 3071 - 3079 (2007). http://dx.doi.org/10.1021/jp065165u

S. Pařez and M. Předota: “Determination of Distance-dependent Viscosity of
Mixtures in Parallel Slabs using Non-equilibrium Molecular Dynamics”, Phys.
Chem. Chem. Phys. 14, 3640-3650 (2012).
http://dx.doi.org/10.1039/c2cp22136e

but now we work with larger flexible molecules and larger systems, which
are not suitable for our code.
Is such a request planned to be implemented in Gromacs?
If not, do you have hint in which source code file(s) we could modify this?
Thank you very much

Ondřej Kroutil

-- 
Ondřej Kroutil
,,  Faculty of Science
   "))' University of South Bohemia
 OOO   Branisovska 1760, Ceske Budejovice, 370 05
  OOO  The Czech Republic
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[gmx-users] Questions about parameters

[abhishek khetan]

Dear gmxers,

After some basic simulations of a box of a non-aqueous solvent, I want to
know your opinion about the meaning of some parameters, the values I have
used for these, and how they affect the accuracy of simulations and their
speed (which at this moment is rather unimportant for me).

I started with a box of 2.21x2.21x2.21 nm3 with (4x4x4=) 64 dimethoxyethane
or DME molecules. The box was created so as to match the exact experimental
density to begin with. First I wanted to do the NVT ensemble with Maxwell
like distribution so I went for a total of 1000 ps md-vv integrator and
nose-hoover thermostat with:
dt = 0.0005
tcoupl = nose-hoover
tau-t  = 5.0
ref-t  = 300

Next I did a NPT ensemble for 1000 ps with the md integrator, but with many
parameters changed as:
tcoupl   = v-rescale
tau-t= 1.0
ref-t= 300
pcoupl   = parrinello-rahman
pcoupltype   = isotropic
tau-p= 2.0
compressibility  = 1.2e-4
ref-p= 1.0
refcoord_scaling = com

I needed to change the parameters in order to make the simulations work,
otherwise there were errors which wouldn't let it start, because certain
tcoupl were not compatible with certain pcoupl or integrators. I *DID NOT
USE position restraints*. My NPT simulations converged to a final box
volume very close to the original. More details in my questions, which are
as follows:

1a. Is it okay (in sense of physical accuracy) to change the tcoupl and
integrator when going from NVT to NPT?
1b. How does the value of tau-t and tau-p affect my accuracy and speed? In
my opinion, over a long time simulation, they shouldn't effect accuracy,
but only speed. I am asking this to confirm if I can change them as I want
in order to prevent the simulations from blowing up.


2a. In one set (NVT followed by NPT) of simulations used constraints = all
bonds and in another set I did not use anything. The simulations with
constraints  = all-bonds is a bit slower. What effect do they have on the
accuracy. In the most ideal case of a god given force-field, I should be
able to get by without using any constraints, or ?
2b. If I do not use any constraints, then does gromacs still ensure that
the individual solvent molecules do not disintegrate ?
2c. When I use constraints = all-bonds, then does gromacs still allow for
the harmonic vibration of the individual bonds within a single molecule?
2.d The volume after NPT with no constraints was 2.20x2.20x2.20 nm3 and the
volume after NPT with contraints = all bonds was 2.22x2.22x2.22 nm3. They
are so close to the original, which should I trust more in terms of
physical reality (essentially same as question 2a.)?

3a. What is way position restraints work? I understand that they introduce
a heavy energy penalty on the movement of atoms, but do they apply this
penalty on the absolute deviation of the atoms' positions or on the
deviation of the atom's positions with respect to the centre of mass of the
respective molecule?
3b. If the absolute positions are restrained, then does this also not mean
that in essence the indivdual molecules can never have Maxwell type
velocity distribution? Would it not be better to have the latter kind of
position restraint where the positions are penalized on their deviations
from the centre of mass of individual molecules but the molecules can have
non-penalized movement.
3c. How do these restraints affect my accuracy?
3d. If I do not restrain the positions of some of the atoms in the
molecule, does gromacs still ensure that the molecules do not disintegrate?
3e. Is there any reason why in the itp file the restraints are of values
1000 and 0 only. Would something in the middle, like 500, make sense?

4a. How does the refcoord_scaling work? when i use 'com', does it mean that
the coordinate are scaled with respect to the COM of the whole system in a
way that even bond lengths within the individual molecules change ?
4b. How important is the value of compressibility? for many common
solvents, this value is not available and I am choosing the value of the
most similar specie. Would that affect the accuracy a lot for liquids,
which have the same order of values (10^-4 to 10^-5 bar^-) ?


-- 
MfG,
abhishek
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Re: [gmx-users] Warning: you have generated 17732 solvent molecules which are not multiple of 11 .

[jkrieger]

I'd suggest creating models with and without residue 508 in the target
sequence. MODELLER should be able to rebuild the loop without residue 508
and then you won't have long bonds. A hole in a protein is not physically
or biologically meaningful. Rather a deletion mutation will end up in the
ribosome inserting the next amino acid and linking it by a normal peptide
bond.

You'd then have to set up the system again from the model and I agree with
Peter that you should check what you're doing against a tutorial to avoid
the solvent error.

Best wishes
James

> My project is on cystic fibrosis 508 del mutation ,what I m trying to do
> is
> that I have taken nuclear binding domain with 508phenylalanine (2bbo.pdb)
> and I deleted that 508 phenylalanine to create a similar situation as what
> occurs in body in case of cystic fibrosis ...after minimization of this
> protein I ll dock the protein with a corrector ...and will see the binding
> energy
> On 18-Mar-2016 6:06 am, "Peter Stern"  wrote:
>
>> As James said, if you are using Discovery Studio it can model missing
>> atoms and residues.  But why are you deleting a residue?  What do you
>> hope
>> to learn from this?  And don't just ignore missing atoms.
>>
>> I also don't understand the genion error, but I don't think you reported
>> it exactly.  Didn't genion ask you to choose a solvent group and did you
>> do
>> that correctly?  I certainly didn't mean that you should choose 1612 sol
>> molecules and 11 Na.  I simply meant that I didn't understand the error
>> message since 17732 is divisible by 11.  I suspect that you didn't
>> choose
>> the correct group for solvent.
>>
>> Since you are a beginner may I suggest that you use one of the many
>> Gromacs tutorials available choosing one appropriate to what you are
>> trying
>> to do?  I am sure that you can find these easily enough with Google.
>>
>> Best regards?
>> Peter
>>
>> Sent from my iPhone
>>
>> > On 17 Mar 2016, at 12:27 PM, Pradip Kaur 
>> wrote:
>> >
>> > actually i m not getting how to proceed futher i m beginner to GROMACS
>> > it would be helpful if you can elaborate the process
>> >
>> >> On 17 March 2016 at 21:54, Pradip Kaur 
>> wrote:
>> >>
>> >> so should i go for sol molecules :1612
>> >> Na :11
>> >>
>> >>> On 17 March 2016 at 21:44, Peter Stern 
>> wrote:
>> >>>
>> >>> Missing atoms in GLU 474 is because the coordinates for the GLU side
>> >>> chain weren't resolved in the crystallographic data and aren't
>> included in
>> >>> the pdb file.  Long bonds are probably because of missing residues.
>> Check
>> >>> the pdb file for MISSING residues and atoms (listed in the header
>> >>> records).  Also, you can't just delete a residue and let Gromacs
>> think
>> that
>> >>> the preceding and following residues are connected (by an unphysical
>> "long"
>> >>> bond).  The same goes for missing residues in the pdb file.
>> >>>
>> >>> I hope that the net charge was -5.999 otherwise, why add Na ions.
>> And
>> as
>> >>> far as I know, 11*1612=17732.
>> >>>
>> >>> Peter Stern
>> >>>
>> >>> Sent from my iPad
>> >>>
>> >>> On 17 במרץ 2016, at 11:08, Pradip Kaur > > >>> kaur.pradip...@gmail.com>> wrote:
>> >>>
>> >>> i am currently working with 2bbo.pdb protein ,i have edited this
>> protein
>> >>> in
>> >>> Discovery studio 4.5 and deleted phenylalanine at 508 position , now
>> i
>> m
>> >>> running molecular dynamics simulation  in GROMACS 5.0.2 bt after
>> running
>> >>> pdb2gmx  with  GROMOS96 53a6 force field Water model :spc216 ,it is
>> >>> showing
>> >>>
>> >>> Warning: Long Bond (161-163 = 1.78456 nm)
>> >>>
>> >>> Warning: Long Bond (840-842 = 0.357037 nm)
>> >>>
>> >>> Warning: Long Bond (2237-2239 = 0.636287 nm)
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom CG is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom CD is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom OE1 is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> WARNING: atom OE2 is missing in residue GLU 474 in the pdb file
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> ---
>> >>>
>> >>> Program pdb2gmx, VERSION 5.0.2
>> >>>
>> >>> Source code file:
>> >>> /build/buildd/gromacs-5.0.2/src/gromacs/gmxpreprocess/pdb2top.cpp,
>> line:
>> >>> 1587
>> >>>
>> >>>
>> >>>
>> >>> Fatal error:
>> >>>
>> >>> There were 4 missing atoms in molecule Protein_chain_A, if you want
>> to
>> use
>> >>> this incomplete topology anyhow, use the option -missing
>> >>>
>> >>> For more information and tips for troubleshooting, please check the
>> >>> GROMACS
>> >>>
>> >>> website at http://www.gromacs.org/Documentation/Errors
>> >>>
>> >>>
>> >>> *But  after ignoring missing atoms ,when i am running grompp command

Re: [gmx-users] simulation a box of water

[Pradip Kaur]

you have to select water molecule for running the simulation .choose water
model SPC nd then run the command. I hope then it will work

On 16 March 2016 at 18:51, Justin Lemkul  wrote:

>
>
> On 3/16/16 8:30 AM, Saeed Nasiri wrote:
>
>> Dear all
>>
>> I want to simulate a box of water (2*2*2 nm with 1401 molecules). Is there
>> difference between using a model for water molecules and importing this
>> molecule from other programs(such as nwchem)?
>> I want to do a small simulation and it is not important to treat water
>> molecules explicitly.
>> I used a water.pdb file to generate the box with this command:
>>
>>
> I'm confused.  You don't need to treat water explicitly, but you're
> building a box of explicit water molecules?  Can you please explain in
> greater detail what you're trying to accomplish?  If you have a custom set
> of water parameters, you need to introduce these yourself in suitable
> GROMACS format.
>
> pdb2gmx generates topologies.  By executing it in the manner below, you
> are essentially telling pdb2gmx "I have water, but don't write a topology
> for water" so pdb2gmx correctly fails.
>
> -Justin
>
>
>
>> *gmx_mpi insert-molecules -ci WATER.pdb -nmol 3000 -box 2 2 2 -o
>> water_box.gro*
>>   ...
>>   
>> Added 467 molecules (out of 3000 requested)
>> Writing generated configuration to water_box.gro
>>
>> Output configuration contains 1401 atoms in 934 residues
>>
>> gcq#247: "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix"
>> (Indeep)
>>
>> after that I want to create topol.gro file, but I got an error ?
>>
>>
>> *gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh*
>>:-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:
>>
>>  GROMACS is written by:
>>   Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar
>> Bjelkmar
>>   Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian
>> Fritsch
>>Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent
>> Hindriksen
>>   Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten
>> Kutzner
>>  Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter
>> Meulenhoff
>> Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
>> Roland Schulz Alexey Shvetsov Michael Shirts Alfons
>> Sijbers
>> Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
>> and the project leaders:
>>  Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:  gmx pdb2gmx, VERSION 5.1.2
>> Executable:   /usr/local/gromacs/bin/gmx_mpi
>> Data prefix:  /usr/local/gromacs
>> Command line:
>>gmx_mpi pdb2gmx -f water_box.gro -o water_box2.gro -ignh
>>
>>
>> Select the Force Field:
>>  From '/usr/local/gromacs/share/gromacs/top':
>>   1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24,
>> 1999-2012, 2003)
>>   2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>>   3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
>> 461-469, 1996)
>>   4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21,
>> 1049-1074, 2000)
>>   5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65,
>> 712-725, 2006)
>>   6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al.,
>> Proteins 78, 1950-58, 2010)
>>   7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>>   8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>>   9: GROMOS96 43a1 force field
>> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
>> 10.1007/s00249-011-0700-9)
>> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 15
>>
>> Using the Oplsaa force field in directory oplsaa.ff
>>
>> Opening force field file
>> /usr/local/gromacs/share/gromacs/top/oplsaa.ff/watermodels.dat
>>
>> Select the Water Model:
>>   1: TIP4P  TIP 4-point, recommended
>>   2: TIP4PEW TIP 4-point with Ewald
>>   3: TIP3P  TIP 3-point
>>   4: TIP5P  TIP 5-point (see http://redmine.gromacs.org/issues/1348 for
>> issues)
>>   5: TIP5P  TIP 5-point improved for Ewald sums
>>   6: SPC

Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[Tsjerk Wassenaar]

Hi James,

Yes, that is possible too. If you need a hand, contact me off-list.

Best,

Tsjerk
On Mar 17, 2016 16:32, "James Starlight"  wrote:

> btwh dont understand clearly the whole methodology
>
> for instance If I have coarse'grained system obtained from the
> martinize tool consisted of the 1) many proteins embedded within big
> bilayer and at the same time 2) FG full atomistic topology for one
> protein (without lipids etc) parametrized via ff wich I am going to
> use in subsequent CG to FG conversion- will it be sufficiant for the
> succesfull FG- CG- FG conversions of the protein7 So will it be
> possible to extract CG protein firstly from the whole CG system via
> editconf and that obtain its FG representation using ./initram.sh?
>
> Thanks!!
>
> 2016-03-17 17:26 GMT+01:00 James Starlight :
> > Yep thanks you are right!
> >
> > It seems that lacking of the FG topology is real problem here.
> > Does the |Reverse transformation| method also require the same input
> > data for back to FG representation including innitial FG topology7
> >
> > Thanks in advance!
> >
> > J.
> >
> > 2016-03-17 17:20 GMT+01:00  :
> >> Hi James,
> >> From the tutorial I sent you:
> >> To run the script we need the following:
> >>
> >> The CG structure to backmapp, provided in CG_posre.gro - The CG
> structure you want to back map.
> >>
> >> A complete fine-grained force field corresponding to all the CG
> molecules in CG_posre.gro. Here we use CHARMM36, see all .itp files
> provided and topol.top, which contains the molecules in the same order they
> are present in CG_posre.gro and with the same names. Note, water and ions
> can be skipped in the .top files as they are automatically detected by
> backward.py. - An AA topology of your system (*itp and *top files in an AA
> representation).
> >>
> >> A .map file in the Mapping directory for all residues and molecules to
> be backmapped (water and ions can also be skipped here as their definitions
> are included in backward.py). - A mapping file that will be use to
> reconstruct your CG structure to a FG one based on the topology.
> >>
> >> According to this, is not posible to reconstruct your system without
> the FG topology.
> >>
> >>
> >> --
> >>
> >> Carlos Navarro Retamal
> >> Ingeniero en Bioinformática
> >> Ph. D (c) en Ciencias Aplicadas.
> >> Centro de Bioinformática y Simulación Molecular
> >> Universidad de Talca
> >> Av. Lircay S/N, Talca, Chile
> >> T: (+56) 712201 798
> >> E: carlos.navarr...@gmail.com o cnava...@utalca.cl
> >>
> >> On March 17, 2016 at 1:12:47 PM, James Starlight (
> jmsstarli...@gmail.com) wrote:
> >>
> >> what I have found from the
> >> ./initram.sh -h
> >>
> >> -f Input coarse grained structure
> >> *FILE: None
> >> -p Input atomistic target topology
> >> *FILE: None
> >>
> >>
> >> does it means that -p should be full atomic topology of the system
> >> (not coarse grained) ? Is so whether is possible to make such CG to FG
> >> conversion having only CG input data
> >>
> >> 2016-03-17 17:04 GMT+01:00 James Starlight :
> >>> Just tested the ./initram.sh script embedded within the
> >>>
> >>> Unfortunatelly for my case It didnt works
> >>>
> >>> 1- I firstly extract the gro file consisted of the protein CG
> >>> representation only from my Cg.gro using below command and selecting
> >>> protein group
> >>> g_editconf -f system.gro -n -o protein.gro
> >>>
> >>> than I edit my topology putting here only protein itp
> >>>
> >>> #include "./params/martini_v2.1.itp"
> >>> #include "./params/D2.itp"
> >>>
> >>> [ system ]
> >>> Single Low D2
> >>>
> >>> [ molecules ]
> >>> D2 1
> >>>
> >>>
> >>> finally than I apply script on those two files
> >>> ./initram.sh -f protein.gro -o aa_charmm.gro -to charmm36 -p
> protein.top
> >>>
> >>>
> >>> obtaining error
> >>>
> >>> ---
> >>> Program g_grompp, VERSION 4.5.7
> >>> Source code file:
> >>> /builddir/build/BUILD/gromacs-4.5.7/src/kernel/grompp.c, line: 523
> >>>
> >>> Fatal error:
> >>> number of coordinates in coordinate file (0-backward.gro, 0)
> >>> does not match topology (backmapped.top, 598)
> >>> For more information and tips for troubleshooting, please check the
> GROMACS
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>> ---
> >>>
> >>> 2016-03-17 16:24 GMT+01:00 James Starlight :
>  Is it better than
> 
> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
>  7 PArticularly for my case I need to convert from CG to FG the
>  structure of GPCR simulated within CG lipids excluding lipids in the
>  final FG model.
> 
>  2016-03-17 15:49 GMT+01:00 :
> > Hi James,
> > There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to
> reconstruct the 

[gmx-users] gmx order index option

[李选选]

Hi,
I have a question of “gmx order” usage. I am studying a membrane system so I 
need calculate the deuterium order parameter. In some older tutorials, they 
said the “gmx order” can be used to do the job. The recommended command is like 
“gmx order -s xx.tpr -f xx.xtc -n xx.ndx -d z -nd deuter.xvg”. However, the gmx 
complain that I did not provide a nr option. I read through the manual of “gmx 
order”, it seems that two index file are necessary, -n and -nr. So what is the 
-nr option? Is this the index file that consists of some generic group?

Thanks a lot in advance.

Xuanxuan
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Re: [gmx-users] simulation a box of water

[Justin Lemkul]

On 3/16/16 3:38 PM, Saeed Nasiri wrote:

Thank you Justin
I don't understand. Do I use the explicit water molecules or the model?


You're going to have to explain what this means.  Either you have water 
molecules or you don't.  If you have water molecules, you have to represent them 
using a force field.  If you want some implicit solvent, you need to delete your 
waters and use appropriate .mdp options for an implicit representation.



and where do I used the "define = -DFLEXIBLE" option?


The .mdp file.


please explain a bit more!



Make sure you've done some tutorials to have a good handle on general concepts.

-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] Domain decomposition error tied to free energy perturbation

[Ryan Muraglia]

Hello,

I have been attempting to carry out some free energy calculations, but to
verify the sanity of my parameters, I decided to test them on a structure I
knew to be stable -- the lysozyme from Lemkul's lysozyme in water tutorial.

I chose the L75A mutation because it is out on the surface to minimize the
"difficulty of the transformation."
Using my regular mdp file (even with my mutatation topology generated with
the pmx package), my minimization runs to completion with no errors.

Once I introduce the following lines to my mdp file:

"
; Free energy calculations
free_energy = yes
delta_lambda = 0 ; no Jarzynski non-eq
calc_lambda_neighbors = 1 ; only calculate energy to immediate neighbors
(suitable for BAR, but MBAR needs all)
sc-alpha = 0.5
sc-coul  = no
sc-power = 1.0
sc-sigma = 0.3
couple-moltype   = Protein_chain_A  ; name of moleculetype to
decouple
couple-lambda0   = vdw-q  ; all interactions
couple-lambda1   = vdw ; remove electrostatics, only vdW
couple-intramol  = no
nstdhdl  = 100

; lambda vectors ; decharging only.
; init_lambda_state   0   1   2   3   4   5   6   7   8   9   10
init_lambda_state = 00
coul_lambdas =0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
vdw_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
bonded_lambdas =  0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; match
vdw
mass_lambdas =0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; match
vdw
temperature_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; not
doing simulated tempering
"

I notice two things:
1) Running grompp to generate the tpr file takes much longer
2) The minimization fails to run due the following error related to domain
decomposition:

"
Fatal error:
There is no domain decomposition for 4 ranks that is compatible with the
given box and a minimum cell size of 5.51109 nm
Change the number of ranks or mdrun option -rdd
Look in the log file for details on the domain decomposition
"

I noted that it lists a two-body bonded interaction with a strangely large
distance:

"
Initial maximum inter charge-group distances:
two-body bonded interactions: 5.010 nm, LJC Pairs NB, atoms 1074 1937
  multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1156 1405
Minimum cell size due to bonded interactions: 5.511 nm
"

Atom 1074 corresponds to a hydrogen off the beta-carbon of proline 70, and
atom 1937 refers to a hydrogen on arginine 128. Neither residue is part of
the protein that is being mutated, and they certainly should not be bonded.
The [bonds] directive in the topology confirms that there should be no
interaction between these atoms.
To force the run to begin to get more information on the nature of the
error, I gave mdrun the -nt 1 option, and got the following warning at the
beginning of the minimization (which goes on to end prematurely prior to
reaching the desired Fmax):

"
WARNING: Listed nonbonded interaction between particles 1 and 195
at distance 2.271 which is larger than the table limit 2.200 nm.
"

I'm at a loss in terms of understanding why the addition of my FEP
parameters is causing this error, and appears to be causing the grompp
parser to decide that there is a bond where there shouldn't be, forcing the
minimimum box size to exceed what makes sense for domain decomposition.

Additional information that may be relevant: I am using the amber99sb
forcefield with explicit tip3p waters. I am attempting steepest descent
minimization. rcoulomb and rvdw are both set to 1.2.

Any advice would be greatly appreciated. Thank you!


-- 
Ryan Muraglia
rmurag...@gmail.com
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[gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[James Starlight]

Dear Gromacs users!

I wonder to ask for some suggestions about possibility of the CG to
full atomistic conversion of sample pdb files extracted from the CG
(Martini based) md trajectories. I will be especially thankful for any
kind of the useful tutorial focused on the subject.

Thanks for help in advance!

J.
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Re: [gmx-users] Reconstruction of atomistic details from coarse-grained-structures

[carlos . navarro87]

Hi James,
Sadly I have no idea. I have never used that method/approximation before.
Hope someone with more experience can answer your last question.
Best,
Carlos

-- 

Carlos Navarro Retamal
Ingeniero en Bioinformática
Ph. D (c) en Ciencias Aplicadas.
Centro de Bioinformática y Simulación Molecular
Universidad de Talca
Av. Lircay S/N, Talca, Chile 
T: (+56) 712201 798
E: carlos.navarr...@gmail.com o cnava...@utalca.cl

On March 17, 2016 at 1:26:24 PM, James Starlight (jmsstarli...@gmail.com) wrote:

Yep thanks you are right!

It seems that lacking of the FG topology is real problem here.
Does the |Reverse transformation| method also require the same input
data for back to FG representation including innitial FG topology7

Thanks in advance!

J.

2016-03-17 17:20 GMT+01:00 :
> Hi James,
> From the tutorial I sent you:
> To run the script we need the following:
>
> The CG structure to backmapp, provided in CG_posre.gro - The CG structure you 
> want to back map.
>
> A complete fine-grained force field corresponding to all the CG molecules in 
> CG_posre.gro. Here we use CHARMM36, see all .itp files provided and 
> topol.top, which contains the molecules in the same order they are present in 
> CG_posre.gro and with the same names. Note, water and ions can be skipped in 
> the .top files as they are automatically detected by backward.py. - An AA 
> topology of your system (*itp and *top files in an AA representation).
>
> A .map file in the Mapping directory for all residues and molecules to be 
> backmapped (water and ions can also be skipped here as their definitions are 
> included in backward.py). - A mapping file that will be use to reconstruct 
> your CG structure to a FG one based on the topology.
>
> According to this, is not posible to reconstruct your system without the FG 
> topology.
>
>
> --
>
> Carlos Navarro Retamal
> Ingeniero en Bioinformática
> Ph. D (c) en Ciencias Aplicadas.
> Centro de Bioinformática y Simulación Molecular
> Universidad de Talca
> Av. Lircay S/N, Talca, Chile
> T: (+56) 712201 798
> E: carlos.navarr...@gmail.com o cnava...@utalca.cl
>
> On March 17, 2016 at 1:12:47 PM, James Starlight (jmsstarli...@gmail.com) 
> wrote:
>
> what I have found from the
> ./initram.sh -h
>
> -f Input coarse grained structure
> *FILE: None
> -p Input atomistic target topology
> *FILE: None
>
>
> does it means that -p should be full atomic topology of the system
> (not coarse grained) ? Is so whether is possible to make such CG to FG
> conversion having only CG input data
>
> 2016-03-17 17:04 GMT+01:00 James Starlight :
>> Just tested the ./initram.sh script embedded within the
>>
>> Unfortunatelly for my case It didnt works
>>
>> 1- I firstly extract the gro file consisted of the protein CG
>> representation only from my Cg.gro using below command and selecting
>> protein group
>> g_editconf -f system.gro -n -o protein.gro
>>
>> than I edit my topology putting here only protein itp
>>
>> #include "./params/martini_v2.1.itp"
>> #include "./params/D2.itp"
>>
>> [ system ]
>> Single Low D2
>>
>> [ molecules ]
>> D2 1
>>
>>
>> finally than I apply script on those two files
>> ./initram.sh -f protein.gro -o aa_charmm.gro -to charmm36 -p protein.top
>>
>>
>> obtaining error
>>
>> ---
>> Program g_grompp, VERSION 4.5.7
>> Source code file:
>> /builddir/build/BUILD/gromacs-4.5.7/src/kernel/grompp.c, line: 523
>>
>> Fatal error:
>> number of coordinates in coordinate file (0-backward.gro, 0)
>> does not match topology (backmapped.top, 598)
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> 2016-03-17 16:24 GMT+01:00 James Starlight :
>>> Is it better than
>>> http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Reverse-transformation
>>> 7 PArticularly for my case I need to convert from CG to FG the
>>> structure of GPCR simulated within CG lipids excluding lipids in the
>>> final FG model.
>>>
>>> 2016-03-17 15:49 GMT+01:00 :
 Hi James,
 There is a nice method (developed by Dr. Tsjerk A. Wassenaar) to 
 reconstruct the atomistic structure from a CG structure.
 Here is the respective tutorial 
 http://md.chem.rug.nl/index.php/tutorials-general-introduction/others#Backward
  (from the MARTINI group), and here is the paper of the back mapping 
 method:
 http://pubs.acs.org/doi/abs/10.1021/ct400617g
 Hope this helps.
 Best,
 Carlos
 --

 Carlos Navarro Retamal
 Ingeniero en Bioinformática
 Ph. D (c) en Ciencias Aplicadas.
 Centro de Bioinformática y Simulación Molecular
 Universidad de Talca
 Av. Lircay S/N, Talca, Chile
 T: (+56) 712201 798
 E: carlos.navarr...@gmail.com o cnava...@utalca.cl

 

Re: [gmx-users] Questions about parameters

[Justin Lemkul]

On 3/16/16 3:13 PM, abhishek khetan wrote:

Dear gmxers,

After some basic simulations of a box of a non-aqueous solvent, I want to
know your opinion about the meaning of some parameters, the values I have
used for these, and how they affect the accuracy of simulations and their
speed (which at this moment is rather unimportant for me).

I started with a box of 2.21x2.21x2.21 nm3 with (4x4x4=) 64 dimethoxyethane
or DME molecules. The box was created so as to match the exact experimental
density to begin with. First I wanted to do the NVT ensemble with Maxwell
like distribution so I went for a total of 1000 ps md-vv integrator and
nose-hoover thermostat with:
dt = 0.0005
tcoupl = nose-hoover
tau-t  = 5.0
ref-t  = 300

Next I did a NPT ensemble for 1000 ps with the md integrator, but with many
parameters changed as:
tcoupl   = v-rescale
tau-t= 1.0
ref-t= 300
pcoupl   = parrinello-rahman
pcoupltype   = isotropic
tau-p= 2.0
compressibility  = 1.2e-4
ref-p= 1.0
refcoord_scaling = com

I needed to change the parameters in order to make the simulations work,
otherwise there were errors which wouldn't let it start, because certain
tcoupl were not compatible with certain pcoupl or integrators. I *DID NOT
USE position restraints*. My NPT simulations converged to a final box
volume very close to the original. More details in my questions, which are
as follows:

1a. Is it okay (in sense of physical accuracy) to change the tcoupl and
integrator when going from NVT to NPT?


Without knowing what errors you were getting, it's hard to say.  Just about all 
combinations should be supported so I don't know why this is necessary.  But in 
any case, any time you change an algorithm, you need to allow sufficient time 
for relaxation.



1b. How does the value of tau-t and tau-p affect my accuracy and speed? In
my opinion, over a long time simulation, they shouldn't effect accuracy,
but only speed. I am asking this to confirm if I can change them as I want
in order to prevent the simulations from blowing up.



It has no effect on speed; it's just a value that goes into a function.  For 
accuracy, you can use ensemble checking tools, e.g. those published by the 
Shirts group.  I suspect they have very little impact overall.




2a. In one set (NVT followed by NPT) of simulations used constraints = all
bonds and in another set I did not use anything. The simulations with
constraints  = all-bonds is a bit slower. What effect do they have on the
accuracy. In the most ideal case of a god given force-field, I should be
able to get by without using any constraints, or ?


Constraints are routinely applied to bonds involving hydrogen to allow dt = 1 fs 
or larger.  People commonly constrain all bonds, though strictly speaking that 
shouldn't be done for certain force fields; the errors should be quite small in 
magnitude.



2b. If I do not use any constraints, then does gromacs still ensure that
the individual solvent molecules do not disintegrate ?


GROMACS does what you tell it.  The integrity of the physical model depends on 
the topology and the algorithms you chose.  Bonds are bonds, and they can't be 
broken or formed, but the simulation can crash if you choose to do something 
physical unstable.



2c. When I use constraints = all-bonds, then does gromacs still allow for
the harmonic vibration of the individual bonds within a single molecule?


No, by definition.


2.d The volume after NPT with no constraints was 2.20x2.20x2.20 nm3 and the
volume after NPT with contraints = all bonds was 2.22x2.22x2.22 nm3. They
are so close to the original, which should I trust more in terms of
physical reality (essentially same as question 2a.)?



The volume of a single snapshot means nothing.  The ensemble average is probably 
indistinguishable, but that's what you should check.  Such a tiny box is going 
to be prone to massive pressure fluctuations, though, so anything related to 
pressure or density is probably unreliable, especially with Parrinello-Rahman.



3a. What is way position restraints work? I understand that they introduce
a heavy energy penalty on the movement of atoms, but do they apply this
penalty on the absolute deviation of the atoms' positions or on the
deviation of the atom's positions with respect to the centre of mass of the
respective molecule?


Depends on the what option you choose for refcoord_scaling.


3b. If the absolute positions are restrained, then does this also not mean
that in essence the indivdual molecules can never have Maxwell type
velocity distribution? Would it not be better to have the latter kind of
position restraint where the positions are penalized on their deviations
from the centre of mass of individual molecules but the molecules can have
non-penalized movement.
3c. How do these restraints affect my accuracy?


Related to both questions, the 

[gmx-users] Using FFTK generated parameter file for Protein-Ligand simulations

[Soumya Lipsa Rath]

Dear Gromacs Users,

I have to run a protein-ligand system. I am using CHARMM36 ff for the
simulation. For generating the parameters for the ligand molecule I used
the forcefield development toolkit of vmd, which gives CHARMM compatible
parameters.

But, I am unable to understand how should I include the parameters I had
obtained. I went through the tutorial files which shows an example of
PRODRG server for generating the itp file, but my ligand contains metal
atoms. I would appreciate if somebody could suggest me how to solve this.

Thanks,
Soumya
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Re: [gmx-users] The bond in molecular type DPPC between atoms 31 C21 y 32 022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 times the time step of 1.0e-01 ps

[Justin Lemkul]

On 3/16/16 1:10 PM, Poncho Arvayo Zatarain wrote:

Hello. I' ḿ simulating a DPPC membrane with TIP3 water model and charmm36 
forcefield and in the grompp of NVT equilibration i have this warning: (Warning 1: 
file topol.top line 24) The bond in molecular type DPPC between atoms 31 C21 y 32 
022 has an estimated oscillational period of 2.1e-02 ps, which is less than 5 
times the time step of 1.0e-01 ps. Maybe you forgot to change the constraints mdp 
option. What can i do to solve this? I attached mu nvt.mdp and topol.top. Also i 
have Note 1: rlist is equal to rvdw or/and rcoulomb. There is no explicit verlet 
buffer. The cluster pair list does have a buffering effect, but choosing a larger 
rlist might be neccesari for good energy conservation.Note 2: 
nstcommlistlong  
 = 1.4; Electrostaticscoulombtype	= PME		; Particle Mesh Ewald for long-range electrostaticspme_order	= 4		; cubic interpolationfourierspacing	= 0.16		; grid spacing for FFT; Relative dielectric constant for the medium and the reaction fieldepsilon_r   = 1epsilon_rf  = 1; Temperature coupling is ontcoupl		= V-rescale	; modified Berendsen thermostattc-grps		= DPPC TIP3 	; two coupling groups - more accuratetau_t		= 0.1	0.1 ; time constant, in psref_t		= 350 	350 ; reference temperature, one for each group, in K; Pressure coupling is offpcoupl		= no 		; no pressure coupling in NVT; Periodic boundary conditionspbc		= xyz		; 3-D PBC; Dispersion correctionDispCorr	= no; Velocity generationgen_vel		= yes		; assign velocities from Maxwell distributiongen_temp	= 350		; temperature for Maxwell distributiongen_seed	= -1		; generate a random seed; COM motion removal; These options remove motion of the protein/bilayer relative to the solv!

ent/ionsns
tcomm   = 1comm-mode= Linearcomm-grps   = DPPC TIP3

topol.top Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7 
psf2itp.py Correspondance:;; j712l...@ku.edu or won...@ku.edu The main 
GROMACS topology file;;
; Include forcefield parameters#include "toppar/charmm36.itp"#include 
"toppar/DPPC.itp"#include "toppar/TIP3.itp"


Please make an effort to make your emails readable by using sensible line 
endings.  This is impossible to go through.


-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] Domain decomposition error tied to free energy perturbation

[Justin Lemkul]

On 3/17/16 8:21 PM, Ryan Muraglia wrote:

Hello,

I have been attempting to carry out some free energy calculations, but to
verify the sanity of my parameters, I decided to test them on a structure I
knew to be stable -- the lysozyme from Lemkul's lysozyme in water tutorial.

I chose the L75A mutation because it is out on the surface to minimize the
"difficulty of the transformation."
Using my regular mdp file (even with my mutatation topology generated with
the pmx package), my minimization runs to completion with no errors.

Once I introduce the following lines to my mdp file:

"
; Free energy calculations
free_energy = yes
delta_lambda = 0 ; no Jarzynski non-eq
calc_lambda_neighbors = 1 ; only calculate energy to immediate neighbors
(suitable for BAR, but MBAR needs all)
sc-alpha = 0.5
sc-coul  = no
sc-power = 1.0
sc-sigma = 0.3
couple-moltype   = Protein_chain_A  ; name of moleculetype to
decouple
couple-lambda0   = vdw-q  ; all interactions
couple-lambda1   = vdw ; remove electrostatics, only vdW
couple-intramol  = no
nstdhdl  = 100

; lambda vectors ; decharging only.
; init_lambda_state   0   1   2   3   4   5   6   7   8   9   10
init_lambda_state = 00
coul_lambdas =0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
vdw_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
bonded_lambdas =  0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; match
vdw
mass_lambdas =0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; match
vdw
temperature_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ; not
doing simulated tempering
"

I notice two things:
1) Running grompp to generate the tpr file takes much longer
2) The minimization fails to run due the following error related to domain
decomposition:

"
Fatal error:
There is no domain decomposition for 4 ranks that is compatible with the
given box and a minimum cell size of 5.51109 nm
Change the number of ranks or mdrun option -rdd
Look in the log file for details on the domain decomposition
"

I noted that it lists a two-body bonded interaction with a strangely large
distance:

"
Initial maximum inter charge-group distances:
 two-body bonded interactions: 5.010 nm, LJC Pairs NB, atoms 1074 1937
   multi-body bonded interactions: 0.443 nm, Proper Dih., atoms 1156 1405
Minimum cell size due to bonded interactions: 5.511 nm
"

Atom 1074 corresponds to a hydrogen off the beta-carbon of proline 70, and
atom 1937 refers to a hydrogen on arginine 128. Neither residue is part of
the protein that is being mutated, and they certainly should not be bonded.
The [bonds] directive in the topology confirms that there should be no
interaction between these atoms.


With "couple-intramol = no" (from the manual):

"All intra-molecular non-bonded interactions for moleculetype couple-moltype are 
replaced by exclusions and explicit pair interactions."


So you have a much larger distance for intramolecular interactions, hence DD 
complains and you are more limited in the number of DD cells that can be 
constructed.  Trying to decouple an entire protein chain is (1) not usually 
reasonable and (2) fraught with algorithmic challenges.



To force the run to begin to get more information on the nature of the
error, I gave mdrun the -nt 1 option, and got the following warning at the
beginning of the minimization (which goes on to end prematurely prior to
reaching the desired Fmax):

"
WARNING: Listed nonbonded interaction between particles 1 and 195
at distance 2.271 which is larger than the table limit 2.200 nm.
"

I'm at a loss in terms of understanding why the addition of my FEP
parameters is causing this error, and appears to be causing the grompp
parser to decide that there is a bond where there shouldn't be, forcing the


It's not magically creating bonds; see above.  grompp is taking forever because 
it has to generate a massive list of exclusions and pairs.



minimimum box size to exceed what makes sense for domain decomposition.



If EM fails, that's usually a dead giveaway that either the topology is unsound 
or the initial coordinates are unsuitable in some way.  Without more 
information, it's hard to guess at what's going on.  Does EM proceed without the 
free energy options turned on?


-Justin


Additional information that may be relevant: I am using the amber99sb
forcefield with explicit tip3p waters. I am attempting steepest descent
minimization. rcoulomb and rvdw are both set to 1.2.

Any advice would be greatly appreciated. Thank you!






--
==

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