Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Hi Mark,

The problem is resolved.

Previously, I was using rlist = rvdw = rcoulomb = 1.2, which leads to high
pressure from NVT run. NPT equilibrated avg box length (7.13927 nm) was
used for NVT run.

But I got correct pressure by using rlist = rvdw = rcoulomb = 1.4 (suitable
for GROMOS force field). NPT equilibrated avg box length (7.2115 nm) is
used for NVT run.

Thanks for your kind replies.

Best regards,
Sudip

On Tue, Nov 15, 2016 at 7:05 PM, Sudip Das  wrote:

> Dear Mark,
>
> I have forgot to mention one point. All the data that are provided in the
> previous mail, are for simulation with rigid water molecules.
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 7:00 PM, Sudip Das  wrote:
>
>> Dear Mark,
>>
>> Sorry if I misunderstood your point. I am aware that GROMOS force field
>> was parametrized to work with rigid water. My aim is also not to use
>> flexible water. I have performed the flexible water simulation just for
>> testing purpose.
>>
>> Also the box length is converged (with a 0.0005 nm fluctuation) after the
>> NPT equilibration run and I have used this average box length for the NVT
>> production run.
>>
>> In the NPT equilibration, physical quantities like temperature, pressure
>> (fluctuating between 1 to 2 bar), energies are behaving well. The same is
>> also true for NVT production run, except pressure which is fluctuation
>> between 500 to 1000 bar with an average of 750-780 bar.
>>
>> I am confused about what could be the reason of this high pressure
>> although other quantities are behaving well.
>>
>> Thanks in advanced for your kind suggestions.
>>
>> Best regards,
>> Sudip
>>
>> On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham 
>> wrote:
>>
>>> Hi,
>>>
>>> That's not what I suggested you need to think about. Lots of things go
>>> into
>>> making a useful physical model, and the fact that so far you think the
>>> pressure is OK is only a tiny part of that. You chose a force field that
>>> was parametrized to work with rigid water. If you use it with something
>>> else, then the burden of proof is on you that your eventual observations
>>> will be a valid model.
>>>
>>> Also 750 bar +/- 1000 or with large drift would not be a significant
>>> observation. But only you know these things. Also, you could well have
>>> chosen a volume that is too small because you didn't measure pressure
>>> appropriately during the end of your equilibration phase.
>>>
>>> Mark
>>>
>>> On Tue, Nov 15, 2016 at 1:19 PM Sudip Das  wrote:
>>>
>>> > Dear Mark,
>>> >
>>> > Thanks for your reply.
>>> >
>>> > As rigid water was not giving reasonable pressure, I have tried with
>>> > flexible one where pressure is behaving well upto 2 ns of NVT
>>> simulation.
>>> >
>>> >
>>> > Here is the details of my system:
>>> >
>>> > System: Protein in water
>>> > # of residues in protein: 188
>>> > # of water molecules: 17876
>>> > # of NA cation: 3
>>> > Box length (after NPT equilibration): 7.13927 nm
>>> >
>>> >
>>> >
>>> > Here is the nvt_production.mdp file:
>>> >
>>> >
>>> > title= Protein-ligand complex NVT production
>>> > ;define  = -DFLEXIBLE
>>> >
>>> > ; Run parameters
>>> > integrator  = md
>>> > nsteps  = 20
>>> > dt  = 0.0005
>>> > nstcomm  = 1
>>> > comm_grps = system
>>> > comm_mode   = linear
>>> >
>>> > ; Output control
>>> > nstxout = 200
>>> > nstvout = 200
>>> > nstenergy = 200
>>> > nstlog   = 200
>>> > energygrps  = system
>>> >
>>> > ; Bond parameters
>>> > continuation= no
>>> > constraints = none
>>> >
>>> > ; Neighborsearching
>>> > ns_type = grid
>>> > nstlist = 5
>>> > rlist   = 1.4
>>> >
>>> > rvdw  = 1.4
>>> > cutoff-scheme = Verlet
>>> > vdwtype   = cut-off
>>> >
>>> > ; Electrostatics
>>> > rcoulomb= 1.4
>>> > coulombtype = PME
>>> > pme_order   = 4
>>> > fourierspacing  = 0.16
>>> >
>>> > ; Temperature coupling
>>> > tcoupl  = nose-hoover
>>> > tc-grps = system
>>> > tau_t   = 1.0
>>> > ref_t   = 300
>>> >
>>> > ; Pressure coupling
>>> > pcoupl  = no
>>> >
>>> > ; Periodic boundary conditions
>>> > pbc = xyz
>>> >
>>> > ; Dispersion correction
>>> > DispCorr= EnerPres
>>> >
>>> > ; Velocity generation
>>> > gen_vel = no
>>> >
>>> >
>>> >
>>> > Best regards,
>>> > Sudip
>>> >
>>> > On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham <
>>> mark.j.abra...@gmail.com>
>>> > wrote:
>>> >
>>> > > Hi,
>>> > >
>>> > > The solvent models are designed to be rigid, use flexible versions
>>> only
>>> > if
>>> > > you know why they will be a good model for you.
>>> > >
>>> > > Measuring pressure can take nanoseconds, but we don't have enough
>>> > > information to know what you've done and its error estimates.
>>> > >
>>> > > Mark
>>> > >
>>> > > On Mon, 14 Nov 2016 17:21 Sudip Das  wrote:
>>> > >
>>> > > > Dear All,
>>> > > >
>>> > > > I am simulating a protein in water with GROMOS96 force field
>>> > (gromos54a7)
>>> > > > and SPC/E water model. After minimiza

Re: [gmx-users] PBC issues with membrane-peptide simulation

[Abhi Acharya]

Dear users,

Well, I have found another solution for avoiding the diffusion through the
periodic boundary in such simulations. Hope this is helpful to others doing
similar work.

Basically, the idea is to apply a biasing potential to the COM of the
peptides to pull them towards the membrane so as to ensure interaction with
the lipid bilayer. Thereafter, normal production simulations can be
performed on the peptide membrane complex. See the following paper:

Li, J., Liu, S., Lakshminarayanan, R., Bai, Y., Pervushin, K., Verma, C.,
and Beuerman, R.W. (2013). Molecular simulations suggest how a branched
antimicrobial peptide perturbs a bacterial membrane and enhances
permeability. Biochim. Biophys. Acta *1828*, 1112–1121.

Best Regards,
Abhishek Acharya



On Thu, Nov 10, 2016 at 12:48 PM, Abhi Acharya 
wrote:

> Sorry for that Mark.
>
> Basically, our experimental studies show that our designed peptides (2-3
> different peptides)  are involved in membrane destabilization but their
> activity (in terms of MIC values) varies. We want to understand the
> molecular underpinnings of the membrane destabilization process and
> possibly explain the variation in activities of the peptides. Therefore, we
> wanted to perform some simulations starting from the point where some
> amount of peptides are randomly added to the simulation box on one side of
> the membrane (about 5 nm away from the upper leaflet) and see how the
> system evolves.
>
> The problem is that some of the peptides diffuse along the z-direction
> such that they exit the simulation box and appear on the other side near to
> the lower leaflet.
>
> Hope this is helpful.
>
> Thanks and Regards,
> Abhishek Acharya
>
>
>
>
>
> On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> You haven't said what you're trying to model, so it's going to be hard for
>> someone to help out :-)
>>
>> Mark
>>
>> On Thu, 10 Nov 2016 05:21 Abhi Acharya  wrote:
>>
>> > Thank you Stephane for your suggestion. Though this seems like a nice
>> > solution to circumvent the problem, but do you think this is the normal
>> way
>> > to go about it? I have never found anyone reporting such a methodology
>> for
>> > membrane peptide simulation. Also, I can anticipate significant
>> increase in
>> > computational costs for a double bilayer system. I have a 800 lipid
>> > molecules in a single bilayer, so this is significant factor for me.
>> >
>> > Thanks and Regards,
>> > Abhishek
>> >
>> > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <
>> stephane.a...@cea.fr
>> > >
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > it is not an issue !! To resolve your problem you could simulate two
>> > > bilayer in box and  insert the peptides between them.
>> > >
>> > > HTH
>> > >
>> > > --
>> > >
>> > > Message: 6
>> > > Date: Wed, 9 Nov 2016 16:07:26 +0530
>> > > From: Abhi Acharya 
>> > > To: gromacs.org_gmx-users@maillist.sys.kth.se
>> > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation
>> > > Message-ID:
>> > > > > > gmail.com>
>> > > Content-Type: text/plain; charset=UTF-8
>> > >
>> > > Dear Gromacs users,
>> > >
>> > > I am trying to simulate a system consisting of a lipid bilayer and few
>> > > peptides. The peptides have been added randomly to the simulation box
>> > only
>> > > on one side of the membrane. I ran a 100 ns simulation of the system
>> > using
>> > > CHARMM36 forcefeild. However, I find that within the first few ns,
>> some
>> > of
>> > > the peptides appear on the other side of the membrane. I think that
>> this
>> > is
>> > > because of the diffusion of the peptides though the periodic boundary.
>> > > Kindly suggest  how to tackle this problem. I have used COM motion
>> > removal
>> > > on the whole system for the said simulation.
>> > >
>> > > Regards,
>> > > Abhishek Acharya
>> > >
>> > >
>> > > --
>> > >
>> > > --
>> > > Gromacs Users mailing list
>> > >
>> > > * Please search the archive at http://www.gromacs.org/
>> > > Support/Mailing_Lists/GMX-Users_List before posting!
>> > >
>> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> > > * For (un)subscribe requests visit
>> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > > send a mail to gmx-users-requ...@gromacs.org.
>> > >
>> > > End of gromacs.org_gmx-users Digest, Vol 151, Issue 32
>> > > **
>> > > --
>> > > Gromacs Users mailing list
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>> > >
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>> > * Please search the archive at
>> > 

Re: [gmx-users] MD simulations of two chains protein

[Khadija Amine]

Hi Mark,

Below, the link to the rmsf plot I had for my protein throughout 20 ns
simulation.

https://www.dropbox.com/s/v67u8iplcyl506q/rmsfmergemut.png?dl=0

The command I used is: gmx rmsf -s XXX.tpr -f XXX.xtc -o rmsf.xvg -oq
rmsf.pdb -res

Thank you

*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Tue, Nov 15, 2016 at 10:50 AM, Khadija Amine  wrote:

> Ok I will try that.
>
> There is a way to specify the regions to plot in RMSF using rms tool?
>
> Thank you
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine 
> wrote:
>
>> Hello,
>>
>> Can someone show me how can I proceed?
>>
>> Thank you
>>
>> *Khadija AMINE*
>>
>>
>> *Computational Biology*
>> *Postdoctoral Research Associate*
>> *Carnegie Mellon University*
>>
>> On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine 
>> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I need your help regarding MD simulation of two chains protein.
>>> The chain A is 2-78 aa, and the chain B is 1-168 aa.
>>>
>>> I started with the pdb file where there is specified names of the two
>>> chains as A and B.
>>>
>>> I did solvation of my system in a cubic box, I tried to open the
>>> pdb file issued from this step I didn't find the column specifying the
>>> chain names.
>>>
>>> I run 20 ns of MD for this protein. The RMSF plot of the protein seems
>>> to be overlapping from 1 to 78 and the rest of the residues flctuation
>>> is good.
>>>
>>> As it is the first time am facing such issues with protein with two
>>> chains, how can I avoid such overlap in RMSF plot?
>>>
>>> Is this linked to the chains numbering issued after writing the topology.
>>>
>>> Thank you
>>>
>>> *Khadija AMINE*
>>>
>>>
>>> *Computational Biology*
>>> *Postdoctoral Research Associate*
>>> *Carnegie Mellon University*
>>>
>>
>>
>
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[gmx-users] Updated CHARMM36 force field files

[Justin Lemkul]

Hi All,

An updated set of CHARMM36 force field files for GROMACS is available from our 
website:


http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

There are several notable changes in this release that may be of interest to 
you.

1. The protein parameter set has been updated to include the CHARMM36m 
modifications to better model intrinsically disordered peptides.  The 
corrections dramatically reduce the incorrect alpha-L sampling that was observed 
with C36.  See Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de 
Groot, B.L., Grubmuller, H., and MacKerell, Jr., A.D. CHARMM36m: an improved 
force field for folded and intrinsically disordered proteins, Nature Methods, 
2016, DOI: 10.1038/nmeth.4067


2. A set of modified RNA nucleotides has been added, see Xu, Y., Vanommeslaeghe, 
K., Aleksandrov, A., MacKerell, Jr., A.D., and

Nilsson, L. Additive CHARMM Force Field for Naturally Occurring Modified
Ribonucleotides, Journal of Computational Chemistry, 2016, 37: 896-912.

3. An improved description of halogen bonding has recently been implemented in 
the CGenFF force field for small drug-like molecules.  The approach includes a 
positively charged lone pair along the C-X axis to more accurately represent 
halogen bonding, as described in Gutierrez, I.S., Lin, F.-Y., Vanommeslaeghe, 
K., Lemkul, J.A., Armacost, K.A., Brooks III, C.L., and MacKerell, Jr., A.D. 
Parametrization of halogen bonds in the CHARMM general force field: Improved 
treatment of ligand-protein interactions, Bioorganic & Medicinal Chemistry, 
2016, 24: 4812-4825.


4. Per user requests on this list, I have included the topologies and parameters 
for all D-amino acids.


5. There are several other fixes and tweaks, including neutral N-terminal 
glycine and other missing parameters that have been brought to my attention over 
time.


Otherwise, the contents are the same as previous releases of the force field 
(carbohydrates, lipids, etc).


If there are any questions or problems, please contact me.  I have run the files 
through my stress test of amino acids, DNA, RNA, lipids, and carbohydrates and 
everything looks correct, but we rely on feedback to make sure everything is 
working smoothly.


The complete contents and pertinent references are given in the forcefield.doc 
file.

Happy simulating!

-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] About Area per lipids in Mixed Membranes

[Justin Lemkul]

On 11/15/16 2:29 PM, Poncho Arvayo Zatarain wrote:



Hello: I want to calculate the area per lipids in DPPC/DPPE membranes of 128
lipids per leafleft. I have a membrane with 128 DPPC and 128 molecules ofDPPE
and Box X and Box Y are 8.846591 and 8.846591 respectivelly. Should i
calculate the area per lipid using (Box X * Box Y)/(#lipids per leafleft)?


That assumes the contributions to the area are equal between the two lipids, 
which may not be correct.  There are methods for estimating the contribution of 
each lipid to the APL, though, e.g. http://www.bevanlab.biochem.vt.edu/GridMAT-MD/



Also i have tha same membrane (128 molecules of DPPC and 128 molecules of
DPPE) but with more than 50 molecules of a drug inside the membrane. Box X
and Box Y are 9.118480 and 9.118480. Should i use Box X * Box Y)/(#lipids per
leafleft) too? I´m using gromacs 5.0.2


No, because the drug may occupy some portion of the membrane surface that has to 
be accounted for.  The above program will do that if set up properly.


-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] No interaction between manually added atoms

[Justin Lemkul]

On 11/15/16 7:44 AM, Kamps, M. wrote:

Dear GMX-users,

I'm experiencing difficulty with my manually added atoms to create a
metallic surface within GROMACS. My goal is to create a surface (at this
point metallic, Al) and let it interact with a protein.
In my current situation I've only modelled the aluminium surface
(non-bonded surface). The EM drops to a minimum in only 8 steps (first red
flag?), the NVT and NPT equilibrium look ok, but during the MD run the
surface disassembles like it is made up of loose sand. There is no
interaction at all between my individual atoms. What did I do wrong? Or
what did I forget to do?

I created the surface by defining one single Aluminium atom in a pdb file,
which i converted via pdb2gmx. To enable this, I added a Al.rtp file to a
CHARMM27 forcefield, this file contains these lines:

[ bondedtypes ]
; bonds  angles  dihedrals  impropers
 1   1  1  1
[ AL ]
 [ atoms ]
; name  type  charge  chargegroup
ALAL   0.000 0

Furthermore, to the atomtypes.atp file I added this line:

AL26.981539 ;Aluminium mass

To the ffnonbonded.itp file I added this line:

AL1326.9815390.000A0.2617500.30

Where the last two numbers relate to the Lennard-Jones potential. Although
these values are not based on any scientific literature (at this point),
they should show some interaction?



Garbage in, garbage out.  If you don't have a basis for knowing that these 
parameters give reasonable behavior, "some interaction" may be exactly what 
you're getting.  Use real parameters, from literature, or otherwise derived 
properly.


For instance, CHARMM-compatible metal parameters for FCC lattice structures can 
be found in:


Hendrik Heinz, R. A. Vaia, B. L. Farmer and R. R. Naik, Accurate Simulation
of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6
Lennard-Jones Potentials, Journal of Physical Chemistry C, 2008, 112, 
17281-17290.


When I put the atom into pdb2gmx this is my output Al.gro file:

ALUMINIUM
1
1AL  AL1   0.000   0.000   0.000
   0.0   0.0   0.0

This atom is then replicated with insert-molecules to form an FCC crystal,
using an xyz coordinate file. The result is a nicely stacked (small slab
of) surface consisting of 256 atoms. The topology file looks like this:

[ moleculetype ]
; Namenrexcl
AL   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   1 AL  rtp AL   q  0.0
 1 AL  1 AL AL  1  026.9815   ;
qtot 0

Including the usual lines such as include water models, ion models etc..
The surface is then put in a box (with 1.5 nm distance to edges, in all
directions) and solvated with tip3p water molecules. Can someone help me?



If you have water, then you need to know if the assigned LJ parameters produce 
meaningful interactions with water.  Solve one problem at a time; deal with the 
pure metal lattice and make sure its properties are reasonable.  Then figure out 
if those parameters are balanced with respect to water interactions.


-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] Atomtype SDMSO not found - GROMACS

[Justin Lemkul]

On 11/15/16 5:22 AM, Manasa Surakala wrote:

I am new to GROMACS, running protein-ligand simulation.

The error is as follows:

*Fatal error:*
*Atomtype SDMSO not found. *

after the command: gmx grompp -f em.mdp -c solv_13948302.gro -p topol.top
-o ions_13948302.tpr

Can you please help me to overcome this error?



GROMOS force fields have SDmso as the atom type.  Types are case-sensitive.

-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] About Area per lipids in Mixed Membranes

[Poncho Arvayo Zatarain]

Hello: I want to calculate the area per lipids in DPPC/DPPE membranes of 128 
lipids per leafleft. I have a membrane with 128 DPPC and 128 molecules ofDPPE 
and Box X and Box Y are 8.846591 and 8.846591 respectivelly. Should i calculate 
the area per lipid using (Box X * Box Y)/(#lipids per leafleft)?
Also i have tha same membrane (128 molecules of DPPC and 128 molecules of DPPE) 
but with more than 50 molecules of a drug inside the membrane. Box X and Box Y 
are 9.118480 and 9.118480. Should i use Box X * Box Y)/(#lipids per leafleft) 
too?
I´m using gromacs 5.0.2
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[gmx-users] Tutorials to apply NMR data on Gromacs calculations of protein struture

[Kat G]

Hi All,

I would like to combine NMR study (specifically relaxation data, RDC and
dihedral restraints) with Gromacs calculations to study possible ensembles
of protein structure.

I tried to search NMR refinement by Gromacs but could not see any tutorial
for this purpose, except one with distance restraints (but we did not have
good NOE data to try). Could anyone help me where can I learn to perform
NMR refinement with Gromacs.

Thanks
Kat
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Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

[Elton Carvalho]

Issue #2077 created, thanks!

On Tue, Nov 15, 2016 at 11:11 AM, Mark Abraham  wrote:
> Hi,
>
> Yes that seems a bit inconsistent. Please file a redmine and include e.g. a
> tarball of suitable inputs to reproduce what's going on within grompp.
>
> Mark
>
> On Tue, Nov 15, 2016 at 3:01 PM Elton Carvalho  wrote:
>
>> Hi, Mark,
>>
>> Actually, there seems to be a bug somewhere, because if I defined
>> three type 9 dihedrals in a file and then I define the same three type
>> 9 dihedrals later on, there should be three warnings: one for each
>> multiplicity. there were only two warnings, which means the first one
>> somehow is silent.
>>
>> I just did a quick test and re-enabled the first file. The versions
>> #included by forcefield.itp and by the .top file are identical. I get
>> two arnings (for multiplicities 2 and 3 like on my first email). If I
>> comment out these terms, but keep the first one on the second file, I
>> get no warnings by grompp.
>>
>> This means that grompp reads the three terms from file 1 (hiopefully
>> adding them up), then reads a bunch of parameters and then reads the
>> first term from file 2, which, according to the documentation (and the
>> other warnings) would  throw a warning and overwrite the prvious
>> term(s). No warning is given and the user cannot be sure whether the
>> term was overriden or added up (depending on where the code branches
>> between these alternatives).
>>
>> Could I file a redmine issue regarding that?
>>
>>
>> On Tue, Nov 15, 2016 at 5:02 AM, Mark Abraham 
>> wrote:
>> > Hi,
>> >
>> > Ok that makes sense. Otherwise it would have seemed like it had to be a
>> > code bug.
>> >
>> > Maybe we could add a warning for including the same file twice? Does
>> > anybody do that deliberately E.g with different preprocessor variables
>> > defined?
>> >
>> > Mark
>> >
>> > On Tue, 15 Nov 2016 00:30 Elton Carvalho  wrote:
>> >
>> >> My apologies,
>> >>
>> >> After careful inspection, I noticed that I had #included a copy of
>> >> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [
>> >> dihedraltypes ] directive is actually loaded twice, hence the
>> >> warnings. Removing the #include from forcefield.itp and keeping it in
>> >> the .top file eliminated the warnings and the resulting dynamics seems
>> >> sane (read: did not explode).
>> >>
>> >> Lesson learned: don't change the standard forcefield definition files
>> >> when doing preliminary testing. Especially in the end of a 12h layover
>> >> between flights.
>> >>
>> >> Thank you for your attention,
>> >> --
>> >> Elton
>> >>
>> >> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho 
>> wrote:
>> >> > Hello, fellow Gromacs Users,
>> >> >
>> >> > I'm trying to model P3DDT with CGenFF according to the instructions at
>> >> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in
>> >> > their website. All this is being done on gromacs 2016.
>> >> >
>> >> > The script converts the .str file generated by paramchem.org to
>> >> > gromacs syntax and units. As a first test, I ran a signle
>> >> > dodecylthiophene molecule through the process and obtained apparently
>> >> > sane .top and .itp files. The .itp file #includes a .prm file, that
>> >> > contains the parameters fitted by the paramchem software.
>> >> >
>> >> > When running gmx grompp (version 2016), I get these two warnings:
>> >> >
>> >> > === GROMPP WARNING BEGIN ===
>> >> >
>> >> > WARNING 1 [file ddt.prm, line 17]:
>> >> >   Overriding Proper Dih. parameters.
>> >> >   Use dihedraltype 9 to allow several multiplicity terms. Only
>> >> consecutive
>> >> >   lines are combined. Non-consective lines overwrite each other.
>> >> >
>> >> >   old:  0 0.8368 1 0 0.8368 1
>> >> >   new: CG2R51   CG2R51CG321CG321 9 0.00
>> >>  1.129680 2
>> >> >
>> >> >
>> >> > WARNING 2 [file ddt.prm, line 18]:
>> >> >   Overriding Proper Dih. parameters.
>> >> >   Use dihedraltype 9 to allow several multiplicity terms. Only
>> >> consecutive
>> >> >   lines are combined. Non-consective lines overwrite each other.
>> >> >
>> >> >   old:  0 1.12968 2 0 1.12968
>> 2
>> >> >   new: CG2R51   CG2R51CG321CG321 9 0.00
>> >>  0.00 3
>> >> >
>> >> > === GROMPP WARNING END ===
>> >> >
>> >> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17
>> >> > and 18 of the reffered file, as follows:
>> >> >
>> >> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)===
>> >> >
>> >> > [ dihedraltypes ]
>> >> > ;  ijkl  func phi0 kphi
>> mult
>> >> >   CG2R51   CG2R51   CG2R51CG321 9   180.0016.736000
>>2
>> >> >CG321   CG2R51   CG2R51   SG2R50 9   180.0029.288000
>>2
>> >> >CG321   CG2R51   CG2R51HGR51 9   180.00 4.184000
>>2
>> >> >   CG2R51   CG2R51CG321CG321 9 0.00 0.836800
>>1
>> >> >   CG2R51   C

Re: [gmx-users] REMD ensemble of states

[Abramyan, Tigran]

Hi Mark,

I understand that at each replica the coordinates of the accepted states are 
saved. I understand that I can calculate different properties of 0.xtc in 
differenr programs, e.g., gromacs, MDTraj, etc., but when it comes down to 
visualization in VMD, for example, in gromacs I don't seem to find a way to 
remove the jumps and superpose the coordinates saved in 0.xtc.

Tigran





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Monday, November 14, 2016 1:20 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD ensemble of states

Hi,

The ensemble at each temperature is intrinsically discontinuous. You can't
make it look continuous. What are you trying to do?

Mark

On Mon, 14 Nov 2016 05:26 Abramyan, Tigran  wrote:

> Thank you Mark,
>
> One more question regarding the centering of the frames at 300 replica
> (0.xtc) using trjconv. I have used a few trjconv options, however do not
> seem to be removing jumps from the original trajectory. For example, the
> command below works for me when applied to the *xtc file produced in
> regular MD, however, with REMD it produces a trajectory which won't be of
> use for example in VMD:
>
>  echo 1 | trjconv -s 0.tpr -f 0.xtc -o 300.xtc -pbc nojump -dt 40
>
> I am assuming I may need to use a combination of tpr files to produce the
> nojump 300.xtc file?
>
> Please advise,
> Thank you very much.
> Tigran
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Tuesday, November 8, 2016 1:15 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] REMD ensemble of states
>
> Yes
>
> On Tue, 8 Nov 2016 18:43 Abramyan, Tigran  wrote:
>
> > Hi Mark,
> >
> > Thanks a lot for your prompt response. So  demux.pl creates continuous
> > trajectories, *_trajout.xtc, but the ensemble of states (lowest energy
> > ensemble, typically of interest in the analysis of REMD results) is saved
> > in the original  0.xtc file produced during REMD before using demux.pl?
> >
> > Thank you,
> > Tigran
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > Abraham 
> > Sent: Tuesday, November 8, 2016 5:53 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] REMD ensemble of states
> >
> > Hi,
> >
> > Mdrun wrote that. You made the trajectories contiguous with the demux.
> >
> > Mark
> >
> > On Tue, 8 Nov 2016 04:55 Abramyan, Tigran  wrote:
> >
> > > Hi,
> > >
> > >
> > > I conducted REMD, and extracted the trajectories via
> > > trjcat -f *.trr -demux replica_index.xvg
> > > And now I was wondering which *.xtc file is the ensemble of states at
> the
> > > baseline replica (lowest temperature replica). Intuitively my guess is
> > that
> > > the numbers in the names of *_trajout.xtc files correspond to the
> replica
> > > numbers starting from the baseline, and hence 0_trajout.xtc is the
> > ensemble
> > > of states at the baseline replica, but I may be wrong.
> > >
> > >
> > > Please suggest.
> > >
> > >
> > > Thank you,
> > >
> > > Tigran
> > >
> > >
> > > --
> > > Tigran M. Abramyan, Ph.D.
> > > Postdoctoral Fellow, Computational Biophysics & Molecular Design
> > > Center for Integrative Chemical Biology and Drug Discovery
> > > Eshelman School of Pharmacy
> > > University of North Carolina at Chapel Hill
> > > Chapel Hill, NC 27599-7363
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? R

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

[Mark Abraham]

Hi,

Yes that seems a bit inconsistent. Please file a redmine and include e.g. a
tarball of suitable inputs to reproduce what's going on within grompp.

Mark

On Tue, Nov 15, 2016 at 3:01 PM Elton Carvalho  wrote:

> Hi, Mark,
>
> Actually, there seems to be a bug somewhere, because if I defined
> three type 9 dihedrals in a file and then I define the same three type
> 9 dihedrals later on, there should be three warnings: one for each
> multiplicity. there were only two warnings, which means the first one
> somehow is silent.
>
> I just did a quick test and re-enabled the first file. The versions
> #included by forcefield.itp and by the .top file are identical. I get
> two arnings (for multiplicities 2 and 3 like on my first email). If I
> comment out these terms, but keep the first one on the second file, I
> get no warnings by grompp.
>
> This means that grompp reads the three terms from file 1 (hiopefully
> adding them up), then reads a bunch of parameters and then reads the
> first term from file 2, which, according to the documentation (and the
> other warnings) would  throw a warning and overwrite the prvious
> term(s). No warning is given and the user cannot be sure whether the
> term was overriden or added up (depending on where the code branches
> between these alternatives).
>
> Could I file a redmine issue regarding that?
>
>
> On Tue, Nov 15, 2016 at 5:02 AM, Mark Abraham 
> wrote:
> > Hi,
> >
> > Ok that makes sense. Otherwise it would have seemed like it had to be a
> > code bug.
> >
> > Maybe we could add a warning for including the same file twice? Does
> > anybody do that deliberately E.g with different preprocessor variables
> > defined?
> >
> > Mark
> >
> > On Tue, 15 Nov 2016 00:30 Elton Carvalho  wrote:
> >
> >> My apologies,
> >>
> >> After careful inspection, I noticed that I had #included a copy of
> >> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [
> >> dihedraltypes ] directive is actually loaded twice, hence the
> >> warnings. Removing the #include from forcefield.itp and keeping it in
> >> the .top file eliminated the warnings and the resulting dynamics seems
> >> sane (read: did not explode).
> >>
> >> Lesson learned: don't change the standard forcefield definition files
> >> when doing preliminary testing. Especially in the end of a 12h layover
> >> between flights.
> >>
> >> Thank you for your attention,
> >> --
> >> Elton
> >>
> >> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho 
> wrote:
> >> > Hello, fellow Gromacs Users,
> >> >
> >> > I'm trying to model P3DDT with CGenFF according to the instructions at
> >> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in
> >> > their website. All this is being done on gromacs 2016.
> >> >
> >> > The script converts the .str file generated by paramchem.org to
> >> > gromacs syntax and units. As a first test, I ran a signle
> >> > dodecylthiophene molecule through the process and obtained apparently
> >> > sane .top and .itp files. The .itp file #includes a .prm file, that
> >> > contains the parameters fitted by the paramchem software.
> >> >
> >> > When running gmx grompp (version 2016), I get these two warnings:
> >> >
> >> > === GROMPP WARNING BEGIN ===
> >> >
> >> > WARNING 1 [file ddt.prm, line 17]:
> >> >   Overriding Proper Dih. parameters.
> >> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> >> consecutive
> >> >   lines are combined. Non-consective lines overwrite each other.
> >> >
> >> >   old:  0 0.8368 1 0 0.8368 1
> >> >   new: CG2R51   CG2R51CG321CG321 9 0.00
> >>  1.129680 2
> >> >
> >> >
> >> > WARNING 2 [file ddt.prm, line 18]:
> >> >   Overriding Proper Dih. parameters.
> >> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> >> consecutive
> >> >   lines are combined. Non-consective lines overwrite each other.
> >> >
> >> >   old:  0 1.12968 2 0 1.12968
> 2
> >> >   new: CG2R51   CG2R51CG321CG321 9 0.00
> >>  0.00 3
> >> >
> >> > === GROMPP WARNING END ===
> >> >
> >> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17
> >> > and 18 of the reffered file, as follows:
> >> >
> >> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)===
> >> >
> >> > [ dihedraltypes ]
> >> > ;  ijkl  func phi0 kphi
> mult
> >> >   CG2R51   CG2R51   CG2R51CG321 9   180.0016.736000
>2
> >> >CG321   CG2R51   CG2R51   SG2R50 9   180.0029.288000
>2
> >> >CG321   CG2R51   CG2R51HGR51 9   180.00 4.184000
>2
> >> >   CG2R51   CG2R51CG321CG321 9 0.00 0.836800
>1
> >> >   CG2R51   CG2R51CG321CG321 9 0.00 1.129680
>2
> >> >   CG2R51   CG2R51CG321CG321 9 0.00 0.00
>3
> >> >   CG2R51CG321CG321CG321 9 0.00 0.16

Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

[Elton Carvalho]

Hi, Mark,

Actually, there seems to be a bug somewhere, because if I defined
three type 9 dihedrals in a file and then I define the same three type
9 dihedrals later on, there should be three warnings: one for each
multiplicity. there were only two warnings, which means the first one
somehow is silent.

I just did a quick test and re-enabled the first file. The versions
#included by forcefield.itp and by the .top file are identical. I get
two arnings (for multiplicities 2 and 3 like on my first email). If I
comment out these terms, but keep the first one on the second file, I
get no warnings by grompp.

This means that grompp reads the three terms from file 1 (hiopefully
adding them up), then reads a bunch of parameters and then reads the
first term from file 2, which, according to the documentation (and the
other warnings) would  throw a warning and overwrite the prvious
term(s). No warning is given and the user cannot be sure whether the
term was overriden or added up (depending on where the code branches
between these alternatives).

Could I file a redmine issue regarding that?


On Tue, Nov 15, 2016 at 5:02 AM, Mark Abraham  wrote:
> Hi,
>
> Ok that makes sense. Otherwise it would have seemed like it had to be a
> code bug.
>
> Maybe we could add a warning for including the same file twice? Does
> anybody do that deliberately E.g with different preprocessor variables
> defined?
>
> Mark
>
> On Tue, 15 Nov 2016 00:30 Elton Carvalho  wrote:
>
>> My apologies,
>>
>> After careful inspection, I noticed that I had #included a copy of
>> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [
>> dihedraltypes ] directive is actually loaded twice, hence the
>> warnings. Removing the #include from forcefield.itp and keeping it in
>> the .top file eliminated the warnings and the resulting dynamics seems
>> sane (read: did not explode).
>>
>> Lesson learned: don't change the standard forcefield definition files
>> when doing preliminary testing. Especially in the end of a 12h layover
>> between flights.
>>
>> Thank you for your attention,
>> --
>> Elton
>>
>> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho  wrote:
>> > Hello, fellow Gromacs Users,
>> >
>> > I'm trying to model P3DDT with CGenFF according to the instructions at
>> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in
>> > their website. All this is being done on gromacs 2016.
>> >
>> > The script converts the .str file generated by paramchem.org to
>> > gromacs syntax and units. As a first test, I ran a signle
>> > dodecylthiophene molecule through the process and obtained apparently
>> > sane .top and .itp files. The .itp file #includes a .prm file, that
>> > contains the parameters fitted by the paramchem software.
>> >
>> > When running gmx grompp (version 2016), I get these two warnings:
>> >
>> > === GROMPP WARNING BEGIN ===
>> >
>> > WARNING 1 [file ddt.prm, line 17]:
>> >   Overriding Proper Dih. parameters.
>> >   Use dihedraltype 9 to allow several multiplicity terms. Only
>> consecutive
>> >   lines are combined. Non-consective lines overwrite each other.
>> >
>> >   old:  0 0.8368 1 0 0.8368 1
>> >   new: CG2R51   CG2R51CG321CG321 9 0.00
>>  1.129680 2
>> >
>> >
>> > WARNING 2 [file ddt.prm, line 18]:
>> >   Overriding Proper Dih. parameters.
>> >   Use dihedraltype 9 to allow several multiplicity terms. Only
>> consecutive
>> >   lines are combined. Non-consective lines overwrite each other.
>> >
>> >   old:  0 1.12968 2 0 1.12968 2
>> >   new: CG2R51   CG2R51CG321CG321 9 0.00
>>  0.00 3
>> >
>> > === GROMPP WARNING END ===
>> >
>> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17
>> > and 18 of the reffered file, as follows:
>> >
>> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)===
>> >
>> > [ dihedraltypes ]
>> > ;  ijkl  func phi0 kphi  mult
>> >   CG2R51   CG2R51   CG2R51CG321 9   180.0016.736000 2
>> >CG321   CG2R51   CG2R51   SG2R50 9   180.0029.288000 2
>> >CG321   CG2R51   CG2R51HGR51 9   180.00 4.184000 2
>> >   CG2R51   CG2R51CG321CG321 9 0.00 0.836800 1
>> >   CG2R51   CG2R51CG321CG321 9 0.00 1.129680 2
>> >   CG2R51   CG2R51CG321CG321 9 0.00 0.00 3
>> >   CG2R51CG321CG321CG321 9 0.00 0.167360 3
>> >   CG2R51CG321CG321 HGA2 9 0.00 0.836800 3
>> >
>> > === ddt.prm RELEVANT SECTION END ===
>> >
>> > As you can see, the dihedraltype is 9 and the different multiplicities
>> > of the "CG2R51   CG2R51CG321CG321" dihedral are on adjacent
>> > lines (16, 17 and 18 of the original file. Note that the first warning
>> > is about overriding the parameters on line 16 with those on line 17,
>

Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear Mark,

I have forgot to mention one point. All the data that are provided in the
previous mail, are for simulation with rigid water molecules.

Best regards,
Sudip

On Tue, Nov 15, 2016 at 7:00 PM, Sudip Das  wrote:

> Dear Mark,
>
> Sorry if I misunderstood your point. I am aware that GROMOS force field
> was parametrized to work with rigid water. My aim is also not to use
> flexible water. I have performed the flexible water simulation just for
> testing purpose.
>
> Also the box length is converged (with a 0.0005 nm fluctuation) after the
> NPT equilibration run and I have used this average box length for the NVT
> production run.
>
> In the NPT equilibration, physical quantities like temperature, pressure
> (fluctuating between 1 to 2 bar), energies are behaving well. The same is
> also true for NVT production run, except pressure which is fluctuation
> between 500 to 1000 bar with an average of 750-780 bar.
>
> I am confused about what could be the reason of this high pressure
> although other quantities are behaving well.
>
> Thanks in advanced for your kind suggestions.
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> That's not what I suggested you need to think about. Lots of things go
>> into
>> making a useful physical model, and the fact that so far you think the
>> pressure is OK is only a tiny part of that. You chose a force field that
>> was parametrized to work with rigid water. If you use it with something
>> else, then the burden of proof is on you that your eventual observations
>> will be a valid model.
>>
>> Also 750 bar +/- 1000 or with large drift would not be a significant
>> observation. But only you know these things. Also, you could well have
>> chosen a volume that is too small because you didn't measure pressure
>> appropriately during the end of your equilibration phase.
>>
>> Mark
>>
>> On Tue, Nov 15, 2016 at 1:19 PM Sudip Das  wrote:
>>
>> > Dear Mark,
>> >
>> > Thanks for your reply.
>> >
>> > As rigid water was not giving reasonable pressure, I have tried with
>> > flexible one where pressure is behaving well upto 2 ns of NVT
>> simulation.
>> >
>> >
>> > Here is the details of my system:
>> >
>> > System: Protein in water
>> > # of residues in protein: 188
>> > # of water molecules: 17876
>> > # of NA cation: 3
>> > Box length (after NPT equilibration): 7.13927 nm
>> >
>> >
>> >
>> > Here is the nvt_production.mdp file:
>> >
>> >
>> > title= Protein-ligand complex NVT production
>> > ;define  = -DFLEXIBLE
>> >
>> > ; Run parameters
>> > integrator  = md
>> > nsteps  = 20
>> > dt  = 0.0005
>> > nstcomm  = 1
>> > comm_grps = system
>> > comm_mode   = linear
>> >
>> > ; Output control
>> > nstxout = 200
>> > nstvout = 200
>> > nstenergy = 200
>> > nstlog   = 200
>> > energygrps  = system
>> >
>> > ; Bond parameters
>> > continuation= no
>> > constraints = none
>> >
>> > ; Neighborsearching
>> > ns_type = grid
>> > nstlist = 5
>> > rlist   = 1.4
>> >
>> > rvdw  = 1.4
>> > cutoff-scheme = Verlet
>> > vdwtype   = cut-off
>> >
>> > ; Electrostatics
>> > rcoulomb= 1.4
>> > coulombtype = PME
>> > pme_order   = 4
>> > fourierspacing  = 0.16
>> >
>> > ; Temperature coupling
>> > tcoupl  = nose-hoover
>> > tc-grps = system
>> > tau_t   = 1.0
>> > ref_t   = 300
>> >
>> > ; Pressure coupling
>> > pcoupl  = no
>> >
>> > ; Periodic boundary conditions
>> > pbc = xyz
>> >
>> > ; Dispersion correction
>> > DispCorr= EnerPres
>> >
>> > ; Velocity generation
>> > gen_vel = no
>> >
>> >
>> >
>> > Best regards,
>> > Sudip
>> >
>> > On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham > >
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > The solvent models are designed to be rigid, use flexible versions
>> only
>> > if
>> > > you know why they will be a good model for you.
>> > >
>> > > Measuring pressure can take nanoseconds, but we don't have enough
>> > > information to know what you've done and its error estimates.
>> > >
>> > > Mark
>> > >
>> > > On Mon, 14 Nov 2016 17:21 Sudip Das  wrote:
>> > >
>> > > > Dear All,
>> > > >
>> > > > I am simulating a protein in water with GROMOS96 force field
>> > (gromos54a7)
>> > > > and SPC/E water model. After minimization followed by NVT
>> > equilibration,
>> > > I
>> > > > performed 2ns of NPT equilibration. From the converged box length I
>> > have
>> > > > taken the average value and set the box length (in
>> npt_equilibrium.gro
>> > > > file) to that value and used this for NVT production run.
>> > > >
>> > > > In the production run, temperature, potential and total energies are
>> > > > reasonable, whereas the pressure is behaving weirdly. I have started
>> > the
>> > > > NVT production run with 1 bar pressure.
>> > > >
>> > > >
>> > > > NVT production run with flexible water (define = -DFLEXIBLE): P = 1
>> to
>> > 5
>> > > > bar
>> > > >
>> > > > NVT production run

Re: [gmx-users] Wrong pressure with rigid water

[Mark Abraham]

Hi,

The box size changed over the NPT equilibration. You can't just use the
average size if that includes the non-equilibrated times.

Mark

On Tue, Nov 15, 2016 at 2:30 PM Sudip Das  wrote:

> Dear Mark,
>
> Sorry if I misunderstood your point. I am aware that GROMOS force field was
> parametrized to work with rigid water. My aim is also not to use flexible
> water. I have performed the flexible water simulation just for testing
> purpose.
>
> Also the box length is converged (with a 0.0005 nm fluctuation) after the
> NPT equilibration run and I have used this average box length for the NVT
> production run.
>
> In the NPT equilibration, physical quantities like temperature, pressure
> (fluctuating between 1 to 2 bar), energies are behaving well. The same is
> also true for NVT production run, except pressure which is fluctuation
> between 500 to 1000 bar with an average of 750-780 bar.
>
> I am confused about what could be the reason of this high pressure although
> other quantities are behaving well.
>
> Thanks in advanced for your kind suggestions.
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > That's not what I suggested you need to think about. Lots of things go
> into
> > making a useful physical model, and the fact that so far you think the
> > pressure is OK is only a tiny part of that. You chose a force field that
> > was parametrized to work with rigid water. If you use it with something
> > else, then the burden of proof is on you that your eventual observations
> > will be a valid model.
> >
> > Also 750 bar +/- 1000 or with large drift would not be a significant
> > observation. But only you know these things. Also, you could well have
> > chosen a volume that is too small because you didn't measure pressure
> > appropriately during the end of your equilibration phase.
> >
> > Mark
> >
> > On Tue, Nov 15, 2016 at 1:19 PM Sudip Das  wrote:
> >
> > > Dear Mark,
> > >
> > > Thanks for your reply.
> > >
> > > As rigid water was not giving reasonable pressure, I have tried with
> > > flexible one where pressure is behaving well upto 2 ns of NVT
> simulation.
> > >
> > >
> > > Here is the details of my system:
> > >
> > > System: Protein in water
> > > # of residues in protein: 188
> > > # of water molecules: 17876
> > > # of NA cation: 3
> > > Box length (after NPT equilibration): 7.13927 nm
> > >
> > >
> > >
> > > Here is the nvt_production.mdp file:
> > >
> > >
> > > title= Protein-ligand complex NVT production
> > > ;define  = -DFLEXIBLE
> > >
> > > ; Run parameters
> > > integrator  = md
> > > nsteps  = 20
> > > dt  = 0.0005
> > > nstcomm  = 1
> > > comm_grps = system
> > > comm_mode   = linear
> > >
> > > ; Output control
> > > nstxout = 200
> > > nstvout = 200
> > > nstenergy = 200
> > > nstlog   = 200
> > > energygrps  = system
> > >
> > > ; Bond parameters
> > > continuation= no
> > > constraints = none
> > >
> > > ; Neighborsearching
> > > ns_type = grid
> > > nstlist = 5
> > > rlist   = 1.4
> > >
> > > rvdw  = 1.4
> > > cutoff-scheme = Verlet
> > > vdwtype   = cut-off
> > >
> > > ; Electrostatics
> > > rcoulomb= 1.4
> > > coulombtype = PME
> > > pme_order   = 4
> > > fourierspacing  = 0.16
> > >
> > > ; Temperature coupling
> > > tcoupl  = nose-hoover
> > > tc-grps = system
> > > tau_t   = 1.0
> > > ref_t   = 300
> > >
> > > ; Pressure coupling
> > > pcoupl  = no
> > >
> > > ; Periodic boundary conditions
> > > pbc = xyz
> > >
> > > ; Dispersion correction
> > > DispCorr= EnerPres
> > >
> > > ; Velocity generation
> > > gen_vel = no
> > >
> > >
> > >
> > > Best regards,
> > > Sudip
> > >
> > > On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > The solvent models are designed to be rigid, use flexible versions
> only
> > > if
> > > > you know why they will be a good model for you.
> > > >
> > > > Measuring pressure can take nanoseconds, but we don't have enough
> > > > information to know what you've done and its error estimates.
> > > >
> > > > Mark
> > > >
> > > > On Mon, 14 Nov 2016 17:21 Sudip Das  wrote:
> > > >
> > > > > Dear All,
> > > > >
> > > > > I am simulating a protein in water with GROMOS96 force field
> > > (gromos54a7)
> > > > > and SPC/E water model. After minimization followed by NVT
> > > equilibration,
> > > > I
> > > > > performed 2ns of NPT equilibration. From the converged box length I
> > > have
> > > > > taken the average value and set the box length (in
> > npt_equilibrium.gro
> > > > > file) to that value and used this for NVT production run.
> > > > >
> > > > > In the production run, temperature, potential and total energies
> are
> > > > > reasonable, whereas the pressure is behaving weirdly. I have
> started
> > > the
> > > > > NVT production run with 1 bar pressure.
> > > > >
> > > > >
> > > >

Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear Mark,

Sorry if I misunderstood your point. I am aware that GROMOS force field was
parametrized to work with rigid water. My aim is also not to use flexible
water. I have performed the flexible water simulation just for testing
purpose.

Also the box length is converged (with a 0.0005 nm fluctuation) after the
NPT equilibration run and I have used this average box length for the NVT
production run.

In the NPT equilibration, physical quantities like temperature, pressure
(fluctuating between 1 to 2 bar), energies are behaving well. The same is
also true for NVT production run, except pressure which is fluctuation
between 500 to 1000 bar with an average of 750-780 bar.

I am confused about what could be the reason of this high pressure although
other quantities are behaving well.

Thanks in advanced for your kind suggestions.

Best regards,
Sudip

On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham 
wrote:

> Hi,
>
> That's not what I suggested you need to think about. Lots of things go into
> making a useful physical model, and the fact that so far you think the
> pressure is OK is only a tiny part of that. You chose a force field that
> was parametrized to work with rigid water. If you use it with something
> else, then the burden of proof is on you that your eventual observations
> will be a valid model.
>
> Also 750 bar +/- 1000 or with large drift would not be a significant
> observation. But only you know these things. Also, you could well have
> chosen a volume that is too small because you didn't measure pressure
> appropriately during the end of your equilibration phase.
>
> Mark
>
> On Tue, Nov 15, 2016 at 1:19 PM Sudip Das  wrote:
>
> > Dear Mark,
> >
> > Thanks for your reply.
> >
> > As rigid water was not giving reasonable pressure, I have tried with
> > flexible one where pressure is behaving well upto 2 ns of NVT simulation.
> >
> >
> > Here is the details of my system:
> >
> > System: Protein in water
> > # of residues in protein: 188
> > # of water molecules: 17876
> > # of NA cation: 3
> > Box length (after NPT equilibration): 7.13927 nm
> >
> >
> >
> > Here is the nvt_production.mdp file:
> >
> >
> > title= Protein-ligand complex NVT production
> > ;define  = -DFLEXIBLE
> >
> > ; Run parameters
> > integrator  = md
> > nsteps  = 20
> > dt  = 0.0005
> > nstcomm  = 1
> > comm_grps = system
> > comm_mode   = linear
> >
> > ; Output control
> > nstxout = 200
> > nstvout = 200
> > nstenergy = 200
> > nstlog   = 200
> > energygrps  = system
> >
> > ; Bond parameters
> > continuation= no
> > constraints = none
> >
> > ; Neighborsearching
> > ns_type = grid
> > nstlist = 5
> > rlist   = 1.4
> >
> > rvdw  = 1.4
> > cutoff-scheme = Verlet
> > vdwtype   = cut-off
> >
> > ; Electrostatics
> > rcoulomb= 1.4
> > coulombtype = PME
> > pme_order   = 4
> > fourierspacing  = 0.16
> >
> > ; Temperature coupling
> > tcoupl  = nose-hoover
> > tc-grps = system
> > tau_t   = 1.0
> > ref_t   = 300
> >
> > ; Pressure coupling
> > pcoupl  = no
> >
> > ; Periodic boundary conditions
> > pbc = xyz
> >
> > ; Dispersion correction
> > DispCorr= EnerPres
> >
> > ; Velocity generation
> > gen_vel = no
> >
> >
> >
> > Best regards,
> > Sudip
> >
> > On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > The solvent models are designed to be rigid, use flexible versions only
> > if
> > > you know why they will be a good model for you.
> > >
> > > Measuring pressure can take nanoseconds, but we don't have enough
> > > information to know what you've done and its error estimates.
> > >
> > > Mark
> > >
> > > On Mon, 14 Nov 2016 17:21 Sudip Das  wrote:
> > >
> > > > Dear All,
> > > >
> > > > I am simulating a protein in water with GROMOS96 force field
> > (gromos54a7)
> > > > and SPC/E water model. After minimization followed by NVT
> > equilibration,
> > > I
> > > > performed 2ns of NPT equilibration. From the converged box length I
> > have
> > > > taken the average value and set the box length (in
> npt_equilibrium.gro
> > > > file) to that value and used this for NVT production run.
> > > >
> > > > In the production run, temperature, potential and total energies are
> > > > reasonable, whereas the pressure is behaving weirdly. I have started
> > the
> > > > NVT production run with 1 bar pressure.
> > > >
> > > >
> > > > NVT production run with flexible water (define = -DFLEXIBLE): P = 1
> to
> > 5
> > > > bar
> > > >
> > > > NVT production run with rigid water: P = 750 to 780 bar
> > > >
> > > >
> > > > Did anyone encountered this kind of problem? I would appreciate your
> > kind
> > > > help in resolving this.
> > > >
> > > > Best regards,
> > > > Sudip
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * C

Re: [gmx-users] Fwd: Error-File must be an ascii script

[RAHUL SURESH]

Thank you

On Tue, 15 Nov 2016 at 5:47 PM, Mark Abraham 
wrote:

> Hi,
>
> The list can't take attachments, so we can't see your script. You need to
> find out how to call the mpirun you're expected to use  - that's a problem
> you and every other user of your cluster needs solved, so please go and ask
> someone who can simultaneously solve the problem for you and for everyone
> else on the cluster. :-)
>
> Mark
>
> On Tue, Nov 15, 2016 at 12:12 PM RAHUL SURESH 
> wrote:
>
> > Hi... this s my script file. And I am totally unaware of my cluster
> > documentation
> >
> > On Tue, Nov 15, 2016 at 1:40 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > No, because I can neither see your script nor read your documentation
> :-)
> > >
> > > Mark
> > >
> > > On Tue, 15 Nov 2016 09:09 RAHUL SURESH 
> wrote:
> > >
> > > > Thank you. Let me check my cluster documentation. Anyway you can help
> > me
> > > to
> > > > correct my script?
> > > >
> > > > On Tue, 15 Nov 2016 at 1:35 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > The error message is probably exactly right - you've incorrectly
> > > > specified
> > > > > the required argument to mpirun -np. This is not a gromacs problem
> -
> > > > check
> > > > > your script and consult your cluster's documentation.
> > > > >
> > > > > Mark
> > > > >
> > > > > On Tue, 15 Nov 2016 05:59 RAHUL SURESH 
> > > wrote:
> > > > >
> > > > > > I want to run my .tpr file in cluster. I have my script file and
> > tpr
> > > > file
> > > > > > in a separate folder  in cluster. But it ends up with the error
> > > > > >
> > > > > > */var/spool/torque/mom_priv/jobs/25552.ramanujam.hpc.org.SC
> > > > > > : line 8: 10: command not
> > found*
> > > > > >
> > > > > >
> > > > >
> > > > *---
> > > -*
> > > > > > *Open MPI has detected that a parameter given to a command line*
> > > > > > *option does not match the expected format:*
> > > > > >
> > > > > > *  Option: np*
> > > > > > *  Param:  gmx_mpi*
> > > > > >
> > > > > > *This is frequently caused by omitting to provide the parameter*
> > > > > > *to an option that requires one. Please check the command line
> and
> > > try
> > > > > > again.*
> > > > > >
> > > > > >
> > > > >
> > > > *---
> > > -*
> > > > > >
> > > > > >
> > > > > > here i have attached my script file.
> > > > > >
> > > > > > Await your help at the earliest Please.
> > > > > >
> > > > > > Thankyou
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > *Regards,*
> > > > > > *Rahul Suresh*
> > > > > > *Research Scholar*
> > > > > > *Bharathiar University*
> > > > > > *Coimbatore*
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > 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:

[gmx-users] No interaction between manually added atoms

[Kamps, M.]

Dear GMX-users,

I'm experiencing difficulty with my manually added atoms to create a
metallic surface within GROMACS. My goal is to create a surface (at this
point metallic, Al) and let it interact with a protein.
In my current situation I've only modelled the aluminium surface
(non-bonded surface). The EM drops to a minimum in only 8 steps (first red
flag?), the NVT and NPT equilibrium look ok, but during the MD run the
surface disassembles like it is made up of loose sand. There is no
interaction at all between my individual atoms. What did I do wrong? Or
what did I forget to do?

I created the surface by defining one single Aluminium atom in a pdb file,
which i converted via pdb2gmx. To enable this, I added a Al.rtp file to a
CHARMM27 forcefield, this file contains these lines:

[ bondedtypes ]
; bonds  angles  dihedrals  impropers
 1   1  1  1
[ AL ]
 [ atoms ]
; name  type  charge  chargegroup
ALAL   0.000 0

Furthermore, to the atomtypes.atp file I added this line:

AL26.981539 ;Aluminium mass

To the ffnonbonded.itp file I added this line:

AL1326.9815390.000A0.2617500.30

Where the last two numbers relate to the Lennard-Jones potential. Although
these values are not based on any scientific literature (at this point),
they should show some interaction?

When I put the atom into pdb2gmx this is my output Al.gro file:

ALUMINIUM
1
1AL  AL1   0.000   0.000   0.000
   0.0   0.0   0.0

This atom is then replicated with insert-molecules to form an FCC crystal,
using an xyz coordinate file. The result is a nicely stacked (small slab
of) surface consisting of 256 atoms. The topology file looks like this:

[ moleculetype ]
; Namenrexcl
AL   3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
; residue   1 AL  rtp AL   q  0.0
 1 AL  1 AL AL  1  026.9815   ;
qtot 0

Including the usual lines such as include water models, ion models etc..
The surface is then put in a box (with 1.5 nm distance to edges, in all
directions) and solvated with tip3p water molecules. Can someone help me?

Mark
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Re: [gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

[Mark Abraham]

Hi,

Yes, probably useful, but unfortunately nobody has wanted to implement it
before now.

You can of course use gmx select to write out a dynamic per-frame selection
of waters, and then gmx trjconv to extract frames that include velocities.
That's not very efficient, but does what you seem to want.

Mark

On Tue, Nov 15, 2016 at 12:16 PM Juan José Galano Frutos 
wrote:

> Hi there:
>
> I am trying to analyze a water shell around a protein, and we are studing
> for instance deltaH in some molecular processes. In this sense as you know
> Enthalpies not only depend on Potential energy but also on Kinetic energies
> and a term pV, so that it is crutial having velocities for calculating
> Kinetic energies. As far as I know the only tool exists to order and
> extract by for instance a distance criterium a water shell around a protein
> is TRJORDER, however this program not print out the velocities in the
> output trajectories so it is impossible to obtain the Enthalpies in my
> anallysis.
>
> Could you suggest to me any solutions...
> Wouldn't be useful to add that functionality to TRJORDER program? Would it
> be?
>
> Thank you very much in advance.
>
>
> Juan José Galano Frutos
>
> Department of Biochemistry and
> Molecular and Cellular Biology,
> Faculty of Sciences,
> University of Zaragoza
> Pedro Cerbuna # 12, 50009
> Zaragoza (Spain)
> +34 976 76 28 06 <+34%20976%2076%2028%2006>
>
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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Re: [gmx-users] Wrong pressure with rigid water

[Mark Abraham]

Hi,

That's not what I suggested you need to think about. Lots of things go into
making a useful physical model, and the fact that so far you think the
pressure is OK is only a tiny part of that. You chose a force field that
was parametrized to work with rigid water. If you use it with something
else, then the burden of proof is on you that your eventual observations
will be a valid model.

Also 750 bar +/- 1000 or with large drift would not be a significant
observation. But only you know these things. Also, you could well have
chosen a volume that is too small because you didn't measure pressure
appropriately during the end of your equilibration phase.

Mark

On Tue, Nov 15, 2016 at 1:19 PM Sudip Das  wrote:

> Dear Mark,
>
> Thanks for your reply.
>
> As rigid water was not giving reasonable pressure, I have tried with
> flexible one where pressure is behaving well upto 2 ns of NVT simulation.
>
>
> Here is the details of my system:
>
> System: Protein in water
> # of residues in protein: 188
> # of water molecules: 17876
> # of NA cation: 3
> Box length (after NPT equilibration): 7.13927 nm
>
>
>
> Here is the nvt_production.mdp file:
>
>
> title= Protein-ligand complex NVT production
> ;define  = -DFLEXIBLE
>
> ; Run parameters
> integrator  = md
> nsteps  = 20
> dt  = 0.0005
> nstcomm  = 1
> comm_grps = system
> comm_mode   = linear
>
> ; Output control
> nstxout = 200
> nstvout = 200
> nstenergy = 200
> nstlog   = 200
> energygrps  = system
>
> ; Bond parameters
> continuation= no
> constraints = none
>
> ; Neighborsearching
> ns_type = grid
> nstlist = 5
> rlist   = 1.4
>
> rvdw  = 1.4
> cutoff-scheme = Verlet
> vdwtype   = cut-off
>
> ; Electrostatics
> rcoulomb= 1.4
> coulombtype = PME
> pme_order   = 4
> fourierspacing  = 0.16
>
> ; Temperature coupling
> tcoupl  = nose-hoover
> tc-grps = system
> tau_t   = 1.0
> ref_t   = 300
>
> ; Pressure coupling
> pcoupl  = no
>
> ; Periodic boundary conditions
> pbc = xyz
>
> ; Dispersion correction
> DispCorr= EnerPres
>
> ; Velocity generation
> gen_vel = no
>
>
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > The solvent models are designed to be rigid, use flexible versions only
> if
> > you know why they will be a good model for you.
> >
> > Measuring pressure can take nanoseconds, but we don't have enough
> > information to know what you've done and its error estimates.
> >
> > Mark
> >
> > On Mon, 14 Nov 2016 17:21 Sudip Das  wrote:
> >
> > > Dear All,
> > >
> > > I am simulating a protein in water with GROMOS96 force field
> (gromos54a7)
> > > and SPC/E water model. After minimization followed by NVT
> equilibration,
> > I
> > > performed 2ns of NPT equilibration. From the converged box length I
> have
> > > taken the average value and set the box length (in npt_equilibrium.gro
> > > file) to that value and used this for NVT production run.
> > >
> > > In the production run, temperature, potential and total energies are
> > > reasonable, whereas the pressure is behaving weirdly. I have started
> the
> > > NVT production run with 1 bar pressure.
> > >
> > >
> > > NVT production run with flexible water (define = -DFLEXIBLE): P = 1 to
> 5
> > > bar
> > >
> > > NVT production run with rigid water: P = 750 to 780 bar
> > >
> > >
> > > Did anyone encountered this kind of problem? I would appreciate your
> kind
> > > help in resolving this.
> > >
> > > Best regards,
> > > Sudip
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
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Re: [gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear Mark,

Thanks for your reply.

As rigid water was not giving reasonable pressure, I have tried with
flexible one where pressure is behaving well upto 2 ns of NVT simulation.


Here is the details of my system:

System: Protein in water
# of residues in protein: 188
# of water molecules: 17876
# of NA cation: 3
Box length (after NPT equilibration): 7.13927 nm



Here is the nvt_production.mdp file:


title= Protein-ligand complex NVT production
;define  = -DFLEXIBLE

; Run parameters
integrator  = md
nsteps  = 20
dt  = 0.0005
nstcomm  = 1
comm_grps = system
comm_mode   = linear

; Output control
nstxout = 200
nstvout = 200
nstenergy = 200
nstlog   = 200
energygrps  = system

; Bond parameters
continuation= no
constraints = none

; Neighborsearching
ns_type = grid
nstlist = 5
rlist   = 1.4

rvdw  = 1.4
cutoff-scheme = Verlet
vdwtype   = cut-off

; Electrostatics
rcoulomb= 1.4
coulombtype = PME
pme_order   = 4
fourierspacing  = 0.16

; Temperature coupling
tcoupl  = nose-hoover
tc-grps = system
tau_t   = 1.0
ref_t   = 300

; Pressure coupling
pcoupl  = no

; Periodic boundary conditions
pbc = xyz

; Dispersion correction
DispCorr= EnerPres

; Velocity generation
gen_vel = no



Best regards,
Sudip

On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham 
wrote:

> Hi,
>
> The solvent models are designed to be rigid, use flexible versions only if
> you know why they will be a good model for you.
>
> Measuring pressure can take nanoseconds, but we don't have enough
> information to know what you've done and its error estimates.
>
> Mark
>
> On Mon, 14 Nov 2016 17:21 Sudip Das  wrote:
>
> > Dear All,
> >
> > I am simulating a protein in water with GROMOS96 force field (gromos54a7)
> > and SPC/E water model. After minimization followed by NVT equilibration,
> I
> > performed 2ns of NPT equilibration. From the converged box length I have
> > taken the average value and set the box length (in npt_equilibrium.gro
> > file) to that value and used this for NVT production run.
> >
> > In the production run, temperature, potential and total energies are
> > reasonable, whereas the pressure is behaving weirdly. I have started the
> > NVT production run with 1 bar pressure.
> >
> >
> > NVT production run with flexible water (define = -DFLEXIBLE): P = 1 to 5
> > bar
> >
> > NVT production run with rigid water: P = 750 to 780 bar
> >
> >
> > Did anyone encountered this kind of problem? I would appreciate your kind
> > help in resolving this.
> >
> > Best regards,
> > Sudip
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] Fwd: Error-File must be an ascii script

[Mark Abraham]

Hi,

The list can't take attachments, so we can't see your script. You need to
find out how to call the mpirun you're expected to use  - that's a problem
you and every other user of your cluster needs solved, so please go and ask
someone who can simultaneously solve the problem for you and for everyone
else on the cluster. :-)

Mark

On Tue, Nov 15, 2016 at 12:12 PM RAHUL SURESH 
wrote:

> Hi... this s my script file. And I am totally unaware of my cluster
> documentation
>
> On Tue, Nov 15, 2016 at 1:40 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > No, because I can neither see your script nor read your documentation :-)
> >
> > Mark
> >
> > On Tue, 15 Nov 2016 09:09 RAHUL SURESH  wrote:
> >
> > > Thank you. Let me check my cluster documentation. Anyway you can help
> me
> > to
> > > correct my script?
> > >
> > > On Tue, 15 Nov 2016 at 1:35 PM, Mark Abraham  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > The error message is probably exactly right - you've incorrectly
> > > specified
> > > > the required argument to mpirun -np. This is not a gromacs problem -
> > > check
> > > > your script and consult your cluster's documentation.
> > > >
> > > > Mark
> > > >
> > > > On Tue, 15 Nov 2016 05:59 RAHUL SURESH 
> > wrote:
> > > >
> > > > > I want to run my .tpr file in cluster. I have my script file and
> tpr
> > > file
> > > > > in a separate folder  in cluster. But it ends up with the error
> > > > >
> > > > > */var/spool/torque/mom_priv/jobs/25552.ramanujam.hpc.org.SC
> > > > > : line 8: 10: command not
> found*
> > > > >
> > > > >
> > > >
> > > *---
> > -*
> > > > > *Open MPI has detected that a parameter given to a command line*
> > > > > *option does not match the expected format:*
> > > > >
> > > > > *  Option: np*
> > > > > *  Param:  gmx_mpi*
> > > > >
> > > > > *This is frequently caused by omitting to provide the parameter*
> > > > > *to an option that requires one. Please check the command line and
> > try
> > > > > again.*
> > > > >
> > > > >
> > > >
> > > *---
> > -*
> > > > >
> > > > >
> > > > > here i have attached my script file.
> > > > >
> > > > > Await your help at the earliest Please.
> > > > >
> > > > > Thankyou
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > *Regards,*
> > > > > *Rahul Suresh*
> > > > > *Research Scholar*
> > > > > *Bharathiar University*
> > > > > *Coimbatore*
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> or
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> > > >
> > > --
> > > Gromacs Users mailing list
> > >
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> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
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> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Error with a ligand molecule by ATB

[이명기]

Thank you. I solved the problem already.
The file provided by ATB had a problem,  and I have fixed it.

2016. 11. 15. 오후 8:13에 "Nikhil Maroli" 님이 작성:

> You might need to check the atom naming in both ligand.gro and *.itp file
> and correct it
> --
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[gmx-users] Is it still not possible trjorder to print out velocities and forces in trr trajectories? It would be really useful..

[Juan José Galano Frutos]

Hi there:

I am trying to analyze a water shell around a protein, and we are studing
for instance deltaH in some molecular processes. In this sense as you know
Enthalpies not only depend on Potential energy but also on Kinetic energies
and a term pV, so that it is crutial having velocities for calculating
Kinetic energies. As far as I know the only tool exists to order and
extract by for instance a distance criterium a water shell around a protein
is TRJORDER, however this program not print out the velocities in the
output trajectories so it is impossible to obtain the Enthalpies in my
anallysis.

Could you suggest to me any solutions...
Wouldn't be useful to add that functionality to TRJORDER program? Would it
be?

Thank you very much in advance.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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Re: [gmx-users] Error with a ligand molecule by ATB

[Nikhil Maroli]

You might need to check the atom naming in both ligand.gro and *.itp file
and correct it
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Re: [gmx-users] Fwd: Error-File must be an ascii script

[RAHUL SURESH]

Hi... this s my script file. And I am totally unaware of my cluster
documentation

On Tue, Nov 15, 2016 at 1:40 PM, Mark Abraham 
wrote:

> Hi,
>
> No, because I can neither see your script nor read your documentation :-)
>
> Mark
>
> On Tue, 15 Nov 2016 09:09 RAHUL SURESH  wrote:
>
> > Thank you. Let me check my cluster documentation. Anyway you can help me
> to
> > correct my script?
> >
> > On Tue, 15 Nov 2016 at 1:35 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > The error message is probably exactly right - you've incorrectly
> > specified
> > > the required argument to mpirun -np. This is not a gromacs problem -
> > check
> > > your script and consult your cluster's documentation.
> > >
> > > Mark
> > >
> > > On Tue, 15 Nov 2016 05:59 RAHUL SURESH 
> wrote:
> > >
> > > > I want to run my .tpr file in cluster. I have my script file and tpr
> > file
> > > > in a separate folder  in cluster. But it ends up with the error
> > > >
> > > > */var/spool/torque/mom_priv/jobs/25552.ramanujam.hpc.org.SC
> > > > : line 8: 10: command not found*
> > > >
> > > >
> > >
> > *---
> -*
> > > > *Open MPI has detected that a parameter given to a command line*
> > > > *option does not match the expected format:*
> > > >
> > > > *  Option: np*
> > > > *  Param:  gmx_mpi*
> > > >
> > > > *This is frequently caused by omitting to provide the parameter*
> > > > *to an option that requires one. Please check the command line and
> try
> > > > again.*
> > > >
> > > >
> > >
> > *---
> -*
> > > >
> > > >
> > > > here i have attached my script file.
> > > >
> > > > Await your help at the earliest Please.
> > > >
> > > > Thankyou
> > > >
> > > >
> > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
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> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > --
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> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
> > --
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> > send a mail to gmx-users-requ...@gromacs.org.
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Atomtype SDMSO not found - GROMACS

[Nikhil Maroli]

HI,

It clearly says Atomtype SDMSO not found.
Check the atomype SDMSO

If it is in ligand check the .itp files
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[gmx-users] Atomtype SDMSO not found - GROMACS

[Manasa Surakala]

I am new to GROMACS, running protein-ligand simulation.

The error is as follows:

*Fatal error:*
*Atomtype SDMSO not found. *

after the command: gmx grompp -f em.mdp -c solv_13948302.gro -p topol.top
-o ions_13948302.tpr

Can you please help me to overcome this error?

Thanks in advance,

Manasa
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Re: [gmx-users] Fwd: Error-File must be an ascii script

[Mark Abraham]

Hi,

No, because I can neither see your script nor read your documentation :-)

Mark

On Tue, 15 Nov 2016 09:09 RAHUL SURESH  wrote:

> Thank you. Let me check my cluster documentation. Anyway you can help me to
> correct my script?
>
> On Tue, 15 Nov 2016 at 1:35 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > The error message is probably exactly right - you've incorrectly
> specified
> > the required argument to mpirun -np. This is not a gromacs problem -
> check
> > your script and consult your cluster's documentation.
> >
> > Mark
> >
> > On Tue, 15 Nov 2016 05:59 RAHUL SURESH  wrote:
> >
> > > I want to run my .tpr file in cluster. I have my script file and tpr
> file
> > > in a separate folder  in cluster. But it ends up with the error
> > >
> > > */var/spool/torque/mom_priv/jobs/25552.ramanujam.hpc.org.SC
> > > : line 8: 10: command not found*
> > >
> > >
> >
> **
> > > *Open MPI has detected that a parameter given to a command line*
> > > *option does not match the expected format:*
> > >
> > > *  Option: np*
> > > *  Param:  gmx_mpi*
> > >
> > > *This is frequently caused by omitting to provide the parameter*
> > > *to an option that requires one. Please check the command line and try
> > > again.*
> > >
> > >
> >
> **
> > >
> > >
> > > here i have attached my script file.
> > >
> > > Await your help at the earliest Please.
> > >
> > > Thankyou
> > >
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > Gromacs Users mailing list
> > >
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> > > posting!
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Re: [gmx-users] Md simulation H-atom trajectory analysis.

[Mark Abraham]

Hi,

On Tue, 15 Nov 2016 06:26 maria khan  wrote:

Dear justin
Thanks for your prompt response.
My results are satisfactory.and i managed the H-atoms by _ignh command.but
i just want to learn its solution by conventional system of gromacs also
thats y i am asking.


That sounds like you're not yet clear on what gmx pdb2gmx -ignh does. Do
read gmx pdb2gmx -h. Your choice of force field dictates what hydrogen
atoms are modelled.

Mark

>From your answer can i say that H-atoms trajectory can be studied either it
is handle by -Ignh command or conventional system??
Before your answer i was thinking that by solving the h-atoms by _ignh
command i ll not be able to study the H-atom trajectory as the software has
ignord it.
Thanks for your honorable guidance.
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Re: [gmx-users] Fwd: Error-File must be an ascii script

[RAHUL SURESH]

Thank you. Let me check my cluster documentation. Anyway you can help me to
correct my script?

On Tue, 15 Nov 2016 at 1:35 PM, Mark Abraham 
wrote:

> Hi,
>
> The error message is probably exactly right - you've incorrectly specified
> the required argument to mpirun -np. This is not a gromacs problem - check
> your script and consult your cluster's documentation.
>
> Mark
>
> On Tue, 15 Nov 2016 05:59 RAHUL SURESH  wrote:
>
> > I want to run my .tpr file in cluster. I have my script file and tpr file
> > in a separate folder  in cluster. But it ends up with the error
> >
> > */var/spool/torque/mom_priv/jobs/25552.ramanujam.hpc.org.SC
> > : line 8: 10: command not found*
> >
> >
> **
> > *Open MPI has detected that a parameter given to a command line*
> > *option does not match the expected format:*
> >
> > *  Option: np*
> > *  Param:  gmx_mpi*
> >
> > *This is frequently caused by omitting to provide the parameter*
> > *to an option that requires one. Please check the command line and try
> > again.*
> >
> >
> **
> >
> >
> > here i have attached my script file.
> >
> > Await your help at the earliest Please.
> >
> > Thankyou
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] MD simulations of two chains protein

[Mark Abraham]

Hi,

It's hard for anyone to know what you're doing and seeing unless you share
actual command lines, and upload your resulting graphs to a file-sharing
service and provide a link (the list does not take attachments)

Mark

On Tue, 15 Nov 2016 08:51 Khadija Amine  wrote:

> Ok I will try that.
>
> There is a way to specify the regions to plot in RMSF using rms tool?
>
> Thank you
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>
> On Tue, Nov 15, 2016 at 10:40 AM, Khadija Amine 
> wrote:
>
> > Hello,
> >
> > Can someone show me how can I proceed?
> >
> > Thank you
> >
> > *Khadija AMINE*
> >
> >
> > *Computational Biology*
> > *Postdoctoral Research Associate*
> > *Carnegie Mellon University*
> >
> > On Mon, Nov 14, 2016 at 2:33 PM, Khadija Amine 
> > wrote:
> >
> >> Dear Gromacs users,
> >>
> >> I need your help regarding MD simulation of two chains protein.
> >> The chain A is 2-78 aa, and the chain B is 1-168 aa.
> >>
> >> I started with the pdb file where there is specified names of the two
> >> chains as A and B.
> >>
> >> I did solvation of my system in a cubic box, I tried to open the
> >> pdb file issued from this step I didn't find the column specifying the
> >> chain names.
> >>
> >> I run 20 ns of MD for this protein. The RMSF plot of the protein seems
> >> to be overlapping from 1 to 78 and the rest of the residues flctuation
> >> is good.
> >>
> >> As it is the first time am facing such issues with protein with two
> >> chains, how can I avoid such overlap in RMSF plot?
> >>
> >> Is this linked to the chains numbering issued after writing the
> topology.
> >>
> >> Thank you
> >>
> >> *Khadija AMINE*
> >>
> >>
> >> *Computational Biology*
> >> *Postdoctoral Research Associate*
> >> *Carnegie Mellon University*
> >>
> >
> >
> --
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Re: [gmx-users] Fwd: Error-File must be an ascii script

[Mark Abraham]

Hi,

The error message is probably exactly right - you've incorrectly specified
the required argument to mpirun -np. This is not a gromacs problem - check
your script and consult your cluster's documentation.

Mark

On Tue, 15 Nov 2016 05:59 RAHUL SURESH  wrote:

> I want to run my .tpr file in cluster. I have my script file and tpr file
> in a separate folder  in cluster. But it ends up with the error
>
> */var/spool/torque/mom_priv/jobs/25552.ramanujam.hpc.org.SC
> : line 8: 10: command not found*
>
> **
> *Open MPI has detected that a parameter given to a command line*
> *option does not match the expected format:*
>
> *  Option: np*
> *  Param:  gmx_mpi*
>
> *This is frequently caused by omitting to provide the parameter*
> *to an option that requires one. Please check the command line and try
> again.*
>
> **
>
>
> here i have attached my script file.
>
> Await your help at the earliest Please.
>
> Thankyou
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] grompp warning: "Overriding Proper Dih. parameters" with type 9 dih.

[Mark Abraham]

Hi,

Ok that makes sense. Otherwise it would have seemed like it had to be a
code bug.

Maybe we could add a warning for including the same file twice? Does
anybody do that deliberately E.g with different preprocessor variables
defined?

Mark

On Tue, 15 Nov 2016 00:30 Elton Carvalho  wrote:

> My apologies,
>
> After careful inspection, I noticed that I had #included a copy of
> this ddt.prm file in charmm36-jun2015.ff/forcefield.itp , so the [
> dihedraltypes ] directive is actually loaded twice, hence the
> warnings. Removing the #include from forcefield.itp and keeping it in
> the .top file eliminated the warnings and the resulting dynamics seems
> sane (read: did not explode).
>
> Lesson learned: don't change the standard forcefield definition files
> when doing preliminary testing. Especially in the end of a 12h layover
> between flights.
>
> Thank you for your attention,
> --
> Elton
>
> On Mon, Nov 14, 2016 at 8:04 PM, Elton Carvalho  wrote:
> > Hello, fellow Gromacs Users,
> >
> > I'm trying to model P3DDT with CGenFF according to the instructions at
> > paramchem.org, running the cgenff_charmm2gmx.py script as provided in
> > their website. All this is being done on gromacs 2016.
> >
> > The script converts the .str file generated by paramchem.org to
> > gromacs syntax and units. As a first test, I ran a signle
> > dodecylthiophene molecule through the process and obtained apparently
> > sane .top and .itp files. The .itp file #includes a .prm file, that
> > contains the parameters fitted by the paramchem software.
> >
> > When running gmx grompp (version 2016), I get these two warnings:
> >
> > === GROMPP WARNING BEGIN ===
> >
> > WARNING 1 [file ddt.prm, line 17]:
> >   Overriding Proper Dih. parameters.
> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> consecutive
> >   lines are combined. Non-consective lines overwrite each other.
> >
> >   old:  0 0.8368 1 0 0.8368 1
> >   new: CG2R51   CG2R51CG321CG321 9 0.00
>  1.129680 2
> >
> >
> > WARNING 2 [file ddt.prm, line 18]:
> >   Overriding Proper Dih. parameters.
> >   Use dihedraltype 9 to allow several multiplicity terms. Only
> consecutive
> >   lines are combined. Non-consective lines overwrite each other.
> >
> >   old:  0 1.12968 2 0 1.12968 2
> >   new: CG2R51   CG2R51CG321CG321 9 0.00
>  0.00 3
> >
> > === GROMPP WARNING END ===
> >
> > But the dihedral mentioned is using dihedraltype 9, in lines 16, 17
> > and 18 of the reffered file, as follows:
> >
> > === ddt.prm RELEVANT SECTION BEGIN (lines 10-21)===
> >
> > [ dihedraltypes ]
> > ;  ijkl  func phi0 kphi  mult
> >   CG2R51   CG2R51   CG2R51CG321 9   180.0016.736000 2
> >CG321   CG2R51   CG2R51   SG2R50 9   180.0029.288000 2
> >CG321   CG2R51   CG2R51HGR51 9   180.00 4.184000 2
> >   CG2R51   CG2R51CG321CG321 9 0.00 0.836800 1
> >   CG2R51   CG2R51CG321CG321 9 0.00 1.129680 2
> >   CG2R51   CG2R51CG321CG321 9 0.00 0.00 3
> >   CG2R51CG321CG321CG321 9 0.00 0.167360 3
> >   CG2R51CG321CG321 HGA2 9 0.00 0.836800 3
> >
> > === ddt.prm RELEVANT SECTION END ===
> >
> > As you can see, the dihedraltype is 9 and the different multiplicities
> > of the "CG2R51   CG2R51CG321CG321" dihedral are on adjacent
> > lines (16, 17 and 18 of the original file. Note that the first warning
> > is about overriding the parameters on line 16 with those on line 17,
> > so this dihedral is not defined somewhere else).  No wildcard dihedral
> > parameters are present in the loaded .itp files.
> >
> > Why does grompp warn me that it's "Overriding Proper Dih. parameters",
> > even though the parameters are entered (to the best of my knowledge)
> > as instructed both in the warning and in Section 5.3.3 of the
> > Reference Manual? How can I check whether it really did override the
> > parameter or added the different terms?
> >
> > Thanks in advance,
> > --
> > Elton Carvalho
>
>
>
> --
> Elton Carvalho
> --
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