Re: [gmx-users] water stretched apart

[Tsjerk Wassenaar]

Hi Chetan,

That's due to PBC. Use trjconv -pbc whole to fix it.

Cheers,

Tsjerk
On May 11, 2014 8:12 AM, "Chetan Mahajan"  wrote:

> Dear All,
>
> I need help interpreting one image, that I am sharing via a link:
>
>
> https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012.46.56%20AM.png
>
> It's a system of TiO2 crystal ( 2160 atoms, positions restrained with
> refcoord-scaling: com), 1 formate ion, 1 sodium ion and 3656 water
> molecules, totaling 13133 atoms overall. As you can see TiO2 slab is at the
> center of the box. What I am concerned about is the few water molecules
> stretched along a long distance (visible via lines) in the snapshot shared
> above. Can anyone throw light on what does it mean or why it is happening?
> Is it bad totally? Any solution, if it is totally bad?
>
> I am using a timestep of 1 fs for entire simulation.
>
> Thank you very much.
>
> regards
> Chetan
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[gmx-users] water stretched apart

[Chetan Mahajan]

Dear All,

I need help interpreting one image, that I am sharing via a link:

https://www.dropbox.com/s/z1dly0jfhlftcmc/Screen%20Shot%202014-05-11%20at%2012.46.56%20AM.png

It's a system of TiO2 crystal ( 2160 atoms, positions restrained with
refcoord-scaling: com), 1 formate ion, 1 sodium ion and 3656 water
molecules, totaling 13133 atoms overall. As you can see TiO2 slab is at the
center of the box. What I am concerned about is the few water molecules
stretched along a long distance (visible via lines) in the snapshot shared
above. Can anyone throw light on what does it mean or why it is happening?
Is it bad totally? Any solution, if it is totally bad?

I am using a timestep of 1 fs for entire simulation.

Thank you very much.

regards
Chetan
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Re: [gmx-users] g_dipoles

[Nilesh Dhumal]

I run g_dipoles for two ionic liquids : 1-Ethyl-3-methylimidazolium
chloride and 1-Ethyl-3-methylimidazolium ethylsulfate. In both the systems
cation is common 1-Ethyl-3-methylimidazolium.

In g_dipoles  comde

static void neutralize_mols(int n,int *index,t_block *mols,t_atom *atom)
{
double mtot,qtot;
int  ncharged,m,a0,a1,a;

ncharged = 0;
for(m=0; mindex[index[m]];
a1 = mols->index[index[m]+1];
mtot = 0;
qtot = 0;
for(a=a0; a 0.01)
ncharged++;
if (mtot > 0) {
/* Remove the net charge at the center of mass */
for(a=a0; a
> On 4/27/14, 4:33 PM, Nilesh Dhumal wrote:
>>>
>>>
>>> On 4/27/14, 4:25 PM, Nilesh Dhumal wrote:
>
> On 4/27/14, 4:01 PM, Nilesh Dhumal wrote:
>> Hello,
>>
>> I run g_dipoles for two different systems (System are ionic
>> liquids).
>>
>> For one system when I run g_dipoles I get following message
>>
>> There are 256 molecules in the selection
>> There are 256 charged molecules in the selection,
>> will subtract their charge at their center of mass
>>
>>
>> and I don't get this message for other system.
>>
>> Why program subtract their charge at their center of mass for one
>> system
>> and not for other.
>>
>
> Based on whatever the topology says, g_dipoles doesn't find a net
> charge
> on
> whatever these molecules are.  Without providing more information -
> what
> the
> molecules/selections are, what the topology(ies) is(are) - that's all
> that
> can
> be surmised at this point.
>
> -Justin
>

 There are 128 cations (EMI) and 128 anions (ETS). Total charge is ZERO

 here is molecular section from topology file.
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 1   3   yes 0.5 0.5

#include "emi.itp"
#include "ets.itp"


[ molecules ]
; Compound#mols
EMI128
ETS128

>>
>> For other system I have different anion. I didn't specify the number of
>> residues in molecular section.
>>
>> [ system ]
>> ; Name
>> Grunge ROck MAChoS t= 2.0
>>
>> [ molecules ]
>> ; Compound#mols
>> Ion 1
>>
>
> So "Ion" is some collection of molecules, or what?  If it's a single
> [moleculetype] composed of multiple molecules, each bearing a net charge
> but
> adding up to zero for the whole [moleculetype], this explains your
> observation.
>   g_dipoles reads "Ion" as being a neutral entity, which is probably not
> correct
> for a program like g_dipoles.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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] GPU in Ubuntu

[Szilárd Páll]

On Sat, May 10, 2014 at 10:40 PM, Albert  wrote:
> it is better to choose a stable Linux for computational work. I recommend
> the following:
>
> Redhat Enterprise, Scientific Linux,SuSE Linux Enterprise
>
> Ubuntu is on not stable enough for professional work according to my own
> experiences.

That is highly debatable, I would personally even consider it a false
statement. I don't intend to debate it, though!

Still, Ubuntu and many other non-commercial Linux distributions are
perfectly fine for "professional" or computational work. In fact,
having a newer kernel, compilers, tools, etc. out of the box (rather
than ancient versions like the default in enterprise distros) is often
a huge plus!

>
>
> On 05/10/2014 10:06 PM, lloyd riggs wrote:
>>
>> Dear All,
>> I recently ran into a problem with a small geforce 610, and aside from
>> woundering if it was worth the effort, found in Ubuntu 13.10 gromacs can not
>> find the GPU.  The Nvidia site found this problem and states to install
>> libcudart.5.5.so or higher, i tried this and the 6.0 as well, with no luck.
>
>
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Re: [gmx-users] GPU in Ubuntu

[Szilárd Páll]

Hi,

First of all, the GeForce 610 is a rather basic card, in fact the most
basic among the low-end ones. Unless the computer it is connected to
is *very* slow (e.g. something like a dual-core CPU from 5+ years
ago), my guess is that using it is not going to improve performance of
a GROMACS simulation.

If you still want to try to get it to work, I suggest cleaning out all
NVIDIA driver installations and doing a fresh installation. After
that, even without CUDA, the GPU should work; e.g. the nvidia-smi
command line tool should list it, it should also be useable to drive a
display, etc. If that all works, there is a good chance that
computational codes will work on it too.


Secondly, I am not aware of any free computational resources that can
be used with GROMACS and I have a feeling that you may not find any
offers for substantial amount of free resources. You could consider
cloud-based resources, e.g. you can get a GPU equipped node from
amazon for $0.0656/h which is about $1.6 per day.

--
Szilárd


On Sat, May 10, 2014 at 10:06 PM, lloyd riggs  wrote:
>
> Dear All,
>
> I recently ran into a problem with a small geforce 610, and aside from
> woundering if it was worth the effort, found in Ubuntu 13.10 gromacs can not
> find the GPU.  The Nvidia site found this problem and states to install
> libcudart.5.5.so or higher, i tried this and the 6.0 as well, with no luck.
> The OS itself also has a hard time finding the GPU, however it is found with
> any comand line tool rather easy as a PCI device.  Any fixes, thoughts or
> suggestions as this is simply for set up for systems (EM, initial system
> setup).
>
> A secound question, does anyone know of server based gromacs, as I am at the
> moment hitting a wall with the universities resources (lack of access for
> wierd reasons) and wanted to persue simulations of a few things.  I am aware
> of Groningens site, but have not found much for gromacs any place else,
> although there are several others with different formating, resulting in
> users are only able to use their (the sites) online analytical tools which
> are usually very limited in scope?  With the Groningen site, the only
> complaint is there is no fine tuning of varied parmeters, which means the
> submission works or does not (ie no setting of mdrun parameters such as
> -rcon, -dd, -mpi , only a .tpr and or pdb  file are submitted to the system)
> It is better than nothing, but just a critique, as it worked for me for
> standard systems, but crashed for me with wierd ligands when I used it
> breifly.
>
> Sincerely,
>
> Stephan Watkins, PhD
>
>
> --
> Gromacs Users mailing list
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[gmx-users] poor minimization?

[Chetan Mahajan]

Hi

I am simulating a system consisting of TiO2 crystal (2160 atoms position
restrained), 3656 water molecules, 1 formate and 1 sodium ion. All of my
energy minimizations (5000 steps or more) are getting over in few seconds
(both for steepest descent as well as conjugate gradient). Would you call
that a poor minimization with following data to add more information? If
yes, what could be done to improve it?

(Also note very high value of the maximum force in all trials)

Steepest Descents did not converge to Fmax < 10 in 5001 steps.
Potential Energy  = -1.8874660e+06
Maximum force =  9.7974286e+02 on atom 2161
Norm of force =  1.2869212e+01

Steepest Descents did not converge to Fmax < 10 in 5001 steps.
Potential Energy  = -1.8869792e+06
Maximum force =  2.2741604e+03 on atom 2161
Norm of force =  2.5534626e+01

Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  1.0e+01
   Number of steps=1
   F-max =  6.04871e+03 on atom 563
   F-Norm=  8.55788e+02

Thanks
Chetan
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Re: [gmx-users] GPU in Ubuntu

[Albert]

it is better to choose a stable Linux for computational work. I 
recommend the following:


Redhat Enterprise, Scientific Linux,SuSE Linux Enterprise

Ubuntu is on not stable enough for professional work according to my own 
experiences.



On 05/10/2014 10:06 PM, lloyd riggs wrote:

Dear All,
I recently ran into a problem with a small geforce 610, and aside from 
woundering if it was worth the effort, found in Ubuntu 13.10 gromacs 
can not find the GPU.  The Nvidia site found this problem and states 
to install libcudart.5.5.so or higher, i tried this and the 6.0 as 
well, with no luck.


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Re: [gmx-users] GPU in Ubuntu

[lloyd riggs]

 

Dear All,

 

I recently ran into a problem with a small geforce 610, and aside from woundering if it was worth the effort, found in Ubuntu 13.10 gromacs can not find the GPU.  The Nvidia site found this problem and states to install libcudart.5.5.so or higher, i tried this and the 6.0 as well, with no luck.  The OS itself also has a hard time finding the GPU, however it is found with any comand line tool rather easy as a PCI device.  Any fixes, thoughts or suggestions as this is simply for set up for systems (EM, initial system setup).

 

A secound question, does anyone know of server based gromacs, as I am at the moment hitting a wall with the universities resources (lack of access for wierd reasons) and wanted to persue simulations of a few things.  I am aware of Groningens site, but have not found much for gromacs any place else, although there are several others with different formating, resulting in users are only able to use their (the sites) online analytical tools which are usually very limited in scope?  With the Groningen site, the only complaint is there is no fine tuning of varied parmeters, which means the submission works or does not (ie no setting of mdrun parameters such as -rcon, -dd, -mpi , only a .tpr and or pdb  file are submitted to the system)  It is better than nothing, but just a critique, as it worked for me for standard systems, but crashed for me with wierd ligands when I used it breifly.

 

Sincerely,

 

Stephan Watkins, PhD

 


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Re: [gmx-users] refcoord-scaling

[Chetan Mahajan]

Hi Mark

We discussed this "refcoord scaling=com not working" quite a bit. With new
version of gromacs 4.6.5, it seemed that com option is working fine.
However, I later found out that it is only for equilibration run and system
does blow up (domain decomposition error) in production run. Again to
revise: I have a system consisting of 13133 atoms ( A TiO2 crystal ( 720
Ti) , 3656 water molecules, 1 formate ion, 1 sodium ion). Atoms in TiO2
crystal are held by position restraints.

In the following you had made a comment that multiple COM and PBC may not
be working well with each other. WHy did you think it's a case of
"multiple" com of TiO2?  I am asking this, since in my TiO2 crystal, we are
not defining any bonds between Ti and O, although we are defining entire
TiO2 crystal to be one molecule. So, we can think of only 1 com.

Thanks
Chetan



On Mon, Mar 24, 2014 at 4:16 AM, Mark Abraham wrote:

> On Mar 24, 2014 1:10 AM, "Chetan Mahajan"  wrote:
> >
> > Dear all:
> >
> > I am trying to get a simulation of water solvated titanium oxide running.
> > When 'all' option is used for refcoord-scaling, simulation runs ok.
> > However, when 'com' option is used for refcoord-scaling, simulation
> crashes
> > with any of the following errors. Could anyone explain to me why is this
> > happening
>
> See the description of com. You didn't tell us what you were restraining,
> so it's hard to help. But I can see multiple com of tio2 and PBC not
> working well together, particularly if you box size is far from best.
>
> > or when each of the options such as 'all', 'com' and 'no' is used?
>
> When you really care about your starting position and need to equilibrate
> in NPT.
>
> Mark
>
> > Thanks a lot!
> > regards
> > Chetan
> >
> >
> > Errors:
> >
> > X particles communicated to PME node Y are more than a cell length out of
> > the domain decomposition cell of their charge group
> >
> > This is another way that mdrun tells you your system is blowing
> > up.
> > In GROMACS version 4.0, domain decomposition was introduced to divide the
> > system into regions containing nearby atoms (for more details, see the
> > manual  or the GROMACS 4
> > paper).
> > If you have particles that are flying across the system, you will get
> this
> > fatal error. The message indicates that some piece of your system is
> > tearing apart (hence out of the "cell of their charge group"). Refer
> > to the Blowing
> > Up  page
> for
> > advice on how to fix this issue.
> >
> >
> > A charge group moved too far between two domain decomposition steps.
> > --
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[gmx-users] dssp installation error

[elham tazikeh]

dear gromacs users
when i run do_dssp program 4.5 and 4.6
i saw below error
plz help me

progran do_dssp, version 4.5.3
source code file:do_dsso.c, line: 521

fatal error:
failed to execute command: /usr/local/bin/dssp -na dd5iLsk0 ddj8721A >
/dev/null2> /dev/null

best regards
elham tazikeh
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Re: [gmx-users] vdw radii in g_sas

[rajat desikan]

Thank you Justin, Tsjerk and Antonio for your detailed answers.

g_sas computes uses the truncation distance for residue contacts by
considering the minimum distance between residues. However, the papers I
referred to has a Calpha-Calpha or Cbeta-Cbeta cutoff of 10-12 angstrom
(default g_sas truncation criteria is 1.5 nm). Can anybody give heuristic
suggestions about the truncation distance value?

Thank you all for your time.


On Sat, May 10, 2014 at 7:15 AM, Antonio Baptista wrote:

> You can indeed compute ff-dependent atomic radii from nonbonded
> parameters, which might be sometimes convenient (e.g., when trying to
> optimize a particular methodology). Some ways to do that are discussed in
> section 2.5 of http://dx.doi.org/10.1021/jp052259f.
>
> However, note that the surfaces, volumes, etc computed by tools like g_sas
> are physically vague properties. They are based on a geometrically
> well-defined but somewhat arbitrary algorithm (Lee-Richards, Connolly,
> etc), an idealized spherical solvent probe, and a vaguely defined set of
> "atomic radii" -- even if you use experimentally-derived "van der Waals
> radii", their relation with the data (and thus their physical meaning) is
> neither straightforward nor unique.
>
> Since the properties that g_sas computes are physically vague, the
> important thing is to not depart too much from the usual methodology and
> allow others to reproduce your results. So, unless you are trying to do
> something unusual (as in the paper cited above), use the default GROMACS
> values and cite the version (which has a unique vdwradii.dat), or use
> instead a familiar set of radii (e.g., Bondi) and cite the corresponding
> paper.
>
> Cheers,
> Antonio
>
>
> On Fri, 9 May 2014, Tsjerk Wassenaar wrote:
>
>  Do mind that the radius for P in PO4 is different from that for P alone.
>>
>> Cheers,
>>
>> Tsjerk
>> On May 9, 2014 10:53 PM, "Justin Lemkul"  wrote:
>>
>>
>>>
>>> On 5/9/14, 3:35 PM, rajat desikan wrote:
>>>
>>>  Thanks Justin. I am curious about the value for a phosphorus atom
 (protein
 in phospholipid bilayer; g_sas issues a warning). Do you know any
 reference
 for experimental values?


  Google knows.
>>>
>>> -Justin
>>>
>>>  On Friday, May 9, 2014, Justin Lemkul  wrote:
>>>



> On 5/9/14, 12:23 PM, rajat desikan wrote:
>
>  Hi All,
>
>> In the local copy of vdwradii.dat for g_sas calculations, the vdw
>> radii
>> are
>> very approximate.
>>
>> Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma =
>> 0.367
>> nm
>> => vdwradius=0.185 nm
>>
>> Is it prudent to replace the values in the local vdwradii.dat with the
>> vdwradii derived from ffnonbonded values? I would love to hear your
>> thoughts/suggestions.
>>
>>
>>  No.  The value of sigma will not give you the van der Waals radius of
>>
> an
> atom. For each force field, the value is different, and it is based on
> optimized intermolecular distances.  I don't think there's a clear way
> to
> turn this into some measure of an atom's size.
>
> If you're concerned that the values in vdwradii.dat are not
> sufficiently
> accurate, replace them with real experimentally determined values.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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  --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
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Re: [gmx-users] membrane protein simulation - ligand introduction

[Justin Lemkul]

On 5/10/14, 4:23 AM, Balasubramanian Suriyanarayanan wrote:

Dear Users

If membrane protein ligand complex needs to simulated in lipid bilayers
then how to introduce ligand and at what step?



It's exactly like 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html, 
then use the complex to build the membrane system.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] Embedded view of the users list

[Justin Lemkul]

On 5/10/14, 12:46 PM, Andrew DeYoung wrote:

Hi,

For the past several years and until a few weeks ago, the GMX-Users List
webpage here ( http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List )
had an embedded "live"/"interactive" view of the list.  Messages were
organized in threads such that when I clicked on a thread, I could see all
posts in the thread on one page.  It also had a nice way to search old
messages and sort them by date, etc.

Could someone please confirm that the embedded "live"/"interactive" view of
the list has been taken down from
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List ?



Yes, it was taken down when Nabble was deactivated.

-Justin


It is fine if it has been taken down, since I can still browse through the
archives here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ ) and I can
search the archives by using google with site:https://mailman-1.sys.kth.se
as Mark suggested.  But I just wanted to make sure that it is not just me
and my browser that no longer sees the embedded "live"/"interactive" view of
the list.

Thank you very much!

Andrew DeYoung
Carnegie Mellon University



--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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] GPU for free energy calculation?

[Szilárd Páll]

Hi,

The Verlet scheme supports free energy calculation in 5.0; it works
with GPUs too, but not in double precision.

However, I suggest you consider first whether you really *need* double
precision. If you do, it may still be beneficial for you to use the
Verlet scheme in 5.0 -- especially if you have a small system that
you'll run single-node case in which you can use OpenMP-only and avoid
DD and related bottlenecks like imbalance.

Cheers,
--
Szilárd


On Sat, May 10, 2014 at 5:46 PM, Albert  wrote:
> Hello:
>
> I am going to calculate relative binding energy of ligands. I am just
> wondering can we use GPU for this task? I remembered that it is highly
> recommended to use double precision for free energy calculation considering
> accuracy, but current GPU version seems doesn't support double precision
> well.
>
> thanks a lot
>
> Albert
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[gmx-users] Embedded view of the users list

[Andrew DeYoung]

Hi,

For the past several years and until a few weeks ago, the GMX-Users List
webpage here ( http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List )
had an embedded "live"/"interactive" view of the list.  Messages were
organized in threads such that when I clicked on a thread, I could see all
posts in the thread on one page.  It also had a nice way to search old
messages and sort them by date, etc. 

Could someone please confirm that the embedded "live"/"interactive" view of
the list has been taken down from
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List ?

It is fine if it has been taken down, since I can still browse through the
archives here (
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/ ) and I can
search the archives by using google with site:https://mailman-1.sys.kth.se
as Mark suggested.  But I just wanted to make sure that it is not just me
and my browser that no longer sees the embedded "live"/"interactive" view of
the list.

Thank you very much! 

Andrew DeYoung
Carnegie Mellon University

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[gmx-users] Conferences in 2014

[Ricardo O. S. Soares]

Hello colleagues, 

I apologize if this list isn't the most appropriate place to such topic, but 
I'm looking for some good conferences/symposiums (etc) about Molecular 
Mechanics, structural biology, computational biology and related areas, and I'd 
like to know if someone has any suggestions. 
Is there some event where the gromacs team, contributors and users as well 
intend to attend this year? 

Thanks, 

Ricardo. 
--- 

Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 
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[gmx-users] GPU for free energy calculation?

[Albert]

Hello:

I am going to calculate relative binding energy of ligands. I am just 
wondering can we use GPU for this task? I remembered that it is highly 
recommended to use double precision for free energy calculation 
considering accuracy, but current GPU version seems doesn't support 
double precision well.


thanks a lot

Albert
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[gmx-users] membrane protein simulation - ligand introduction

[Balasubramanian Suriyanarayanan]

Dear Users

If membrane protein ligand complex needs to simulated in lipid bilayers
then how to introduce ligand and at what step?

regards

-- 
B.Suriyanarayanan
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