[gmx-users] Re: Constraints not working in pull code (sometimes, sometimes not)

[Krapnik]

Dear Justin
Thank you for your responses, but it still is not clear to me why is that
happening

> I don't see any real problem here.  The DOPC membrane probably holds its
shape
> better than the octanol slab and thus the reference position (which
determines
> the constraint) is less mobile.

That is certain. When we were running free simulation, the box started to
narrow. Therefore we have frozen the box in xy plane.

> As such, the constraint is more stable in DOPC
> than in octanol.  The slight bump in the octanol system amounts to a
change of
> 0.16%, which I'd say is quite small.

The trouble is, that during next 10 ns the distance was between 2.0 - 4.0
and molecule moved outside of the ocatnol slab and inside, which is then
useless for calculation of PMF.

> You're also looking at the first few
>frames of the simulation, which may amount to equilibration, but you
haven't
> mentioned if you've done anything prior to this run.

Previously, a free simulation with molecule on slab was run for 20 ns, from
which frame with small molecule at specidied depth was taken, so I suppose,
that the start is equilibrated.

> As long as there is no systematic change in position, I'd say there's no
problem.

Unfortunately, there is as I have said before.

-Justin

Dear Chris,
thank you for responses as well.

> I agree that Justin is probably correct, although constraints should
> technically work just fine with a highly dynamic reference group. Any
> problems should show up as the system blowing up, but not in correctly
> setting the position.

I hope, that the position is set up ok, as it stays steady in DOPC.

> I think that the problems can arise, however,
> when you have multiple competing constraints. You might, for example,
> try without constraining the octane bonds -- I think that you should
> get perfect match in that case.

I will try.
The erroneous movement of molecule seems to be enhanced within XY-plane
frozen.
The curious thing is however, that when I did not constrain size of
xy-plane, then the distance to the COM of slab is not changing much (only
last digit changes), which in comparison to frozen XY-plane, where there is
huge movement above the slab and within is rather ok to me. Unfortunately, I
have the issue with narrowing of the box in the unconstrained XYplane
simulation, which also destroys any attempts for PMF as I have mentioned
before.

> Also, it is worth comparing in single
> and double precision.

I will try this either.

> Still, I am not sure that you actually did a proper comparison for the
> following 2 reasons:
>1. you have apparently different masses for the pulled group:
> Pull group 1:15 atoms, mass   194.194
> Pull group 1:15 atoms, mass   146.146

The difference is not much in my opinion, while molecules tested are similar
in size and are run in DOPC ok both of them.

> 2. you used very different starting depth offsets: -2.81855 is not
> very close to -1.60929

The difference is in the size of OCT slab (thick) and DOPC (narrow) and the
trouble is in the vicinity of the water phase, so the distances are (and
should be) different.

> PS: I would personally prefer if you avoided jumping directly to a bug report
unless you are sure of it. There is always at least the
> possibility that you are not using the code correctly.

Certainly and I appreciate two directions you gave me to try - at least I
will look inside octanol topology since I did not used octanol before our
tries of logP. However, I did not say anything about bug (I even searched
for term in my mail and I did not find it)

But how to set the box properly then?

> Chris.

Thank you both
Karel

-- 
Zdraví skoro zdravý
Karel "Krápník" Berka


RNDr. Karel Berka, Ph.D.
Palacký University in Olomouc
Faculty of Science
Department of Physical Chemistry
tř. 17. listopadu 1192/12
771 46 Olomouc
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Re: [gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

Hi Justin
I prepared a box of SOL and arginine Hydrochloride. But when I solvate my
protein with this box now the positively charged arginine is as solvent and
this causes problem in grompp. It gives error like "No such Molecule types
ARG" etc. Solvating arginine with water and preparing a box was without
error. which forcefield in gromacs has inbuilt .itp file for free amino acid
which I can include in my .top file.
Shahid Nayeem

On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Dear All I am trying to find the topology and parameterof free Arginine
>> Hydrchloride molecule in gromacs force-field format. Developing it in
>> Pro-Drg will not serve as  I will need some other parametrization tool to
>> check it charges. If someone can help, I will be grateful.
>>
>
> Isn't this just a protonated arginine (normal state for neutral pH) with a
> chloride counterion?  There's nothing special about it, just run a
> coordinate file through pdb2gmx with the force field of your choice.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
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Re: [gmx-users] Arginine_Hydrochloride topology

[Mark Abraham]

On 11/08/2011 7:24 PM, shahid nayeem wrote:

Hi Justin
I prepared a box of SOL and arginine Hydrochloride. But when I solvate 
my protein with this box now the positively charged arginine is as 
solvent and this causes problem in grompp. It gives error like "No 
such Molecule types ARG" etc. Solvating arginine with water and 
preparing a box was without error. which forcefield in gromacs has 
inbuilt .itp file for free amino acid which I can include in my .top file.


See http://www.gromacs.org/Documentation/How-tos/Multiple_Chains. 
Pre-position the non-water molecules, use pdb2gmx, solvate.


Mark


Shahid Nayeem

On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul > wrote:




shahid nayeem wrote:

Dear All I am trying to find the topology and parameterof free
Arginine Hydrchloride molecule in gromacs force-field format.
Developing it in Pro-Drg will not serve as  I will need some
other parametrization tool to check it charges. If someone can
help, I will be grateful.


Isn't this just a protonated arginine (normal state for neutral
pH) with a chloride counterion?  There's nothing special about it,
just run a coordinate file through pdb2gmx with the force field of
your choice.

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Selenomethionine in pdb file

[Mark Abraham]

On 11/08/2011 2:10 PM, R.Vidya Rajendran (10PHD013) wrote:

Hello Friends,

I would like to do simulation of a protein containing
'selenomethionine' [MSE] in coordinate file, during the first step of
pdb2gmx this residue is not recognizing by any of the force field and
getting fatal error 'Residue 'MSE' not found in residue topology
database'.

Please help me to rectify this problem


See http://www.gromacs.org/Documentation/Errors, like a recent version 
of GROMACS will have suggested that you do.


Mark


tahnks.


regards
vidya


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Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Mark Abraham]

On 11/08/2011 1:45 AM, Da-Wei Li wrote:

Dear Mark

Could you please help me out? I can send you the trajectory (1000 
snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3.


Not unless you can show me a shell script and .mdp file that can take 
your original trajectory, do my suggested procedure and produce your 
observed output. Otherwise, the chance of user error is a thousand times 
more likely than a GROMACS problem.


Mark



I  checked the pdb file in UCSF Chimera and didn't find any crash. I 
have about 10 snapshot that has high vdw energy.


best,

dawei



On Wed, Aug 10, 2011 at 11:32 AM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 11/08/2011 1:18 AM, Da-Wei Li wrote:

Dear Mark

That is my thought too.To test this possibility, I created a mdp
file without PBC and use trjconv -pbc nojump to make whole
protein. >From visualization in UCSF Chimera, the trajectory
looks fine. But I still have some snapshot that have very high
vdw energy.


If all you've done is strip water, make molecules whole with
trjconv -nojump from a reference configuration that had whole
molecules, and use pbc = no in the .mdp file, then that sounds
impossible.

Mark



best

dawei

On Wed, Aug 10, 2011 at 11:12 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>> wrote:

On 11/08/2011 12:29 AM, Da-Wei Li wrote:

Dear Gromacs users:

I recently tried some MM/PBSA stuff using the rerun
function of mdrun and GBSA model. All water molecules are
stripped off the trajectory file.

However, when I examine the different energy term, it is
disturbing that short range vdw energy of some snapshot
are very high (> 1000 kj/mol) while others snapshots
typically have a value around -2000 kj/mol.


Something is badly wrong - perhaps your treatment of
periodicity in the rerun - but we don't have anywhere near
enough information to know.



It is more disturbing that if I do a fitting or pbc
nojump on the trajectory first, I will get very different
 short range vdw for some of the snapshots. All other
energy terms are un-affected.

I believe fitting or no-jump processing shall not change
the energy at all.

Any one has idea about this?


As above.

Mark
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Re: [gmx-users] VMD_PLUGIN_PATH

[Mark Abraham]

On 10/08/2011 1:21 PM, PAUL NEWMAN wrote:

Hi Gromacs Users,

I am using the gromacs analysing tools to analyze my DCD file produced 
by NAMD. I set up the VMD_PLUGIN_PATH before running however I got the 
error that the VMD_PLUGIN_PATH was not set up. Can anyone give me a 
hand? Please see below the details. Thanks for the help


export VMD_PLUGIN_PATH=/home/pet/vmd/1.9/plugins/molfile


Are you using a shell where this works? What does "echo 
$VMD_PLUGIN_PATH" say afterwards?


Mark



g_gyrate_d -f protein.dcd -s ../IN/protein.pdb



The file format of protein.dcd is not a known trajectory format to 
GROMACS.

Please make sure that the file is a trajectory!
GROMACS will now assume it to be a trajectory and will try to open it 
using the VMD plug-ins.
This will only work in case the VMD plugins are found and it is a 
trajectory format supported by VMD.


No VMD Plugins found
Set the environment variable VMD_PLUGIN_PATH to the molfile folder 
within the

VMD installation.
The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to 
match.


---
Program g_gyrate_d, VERSION 4.5.3
Source code file: trxio.c, line: 867

Fatal error:
Not supported in read_first_frame: protein.dcd
For more information and tips for troubleshooting, please check the 
GROMACS

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

"Lets Kill the Fucking Band"  (Tom Savini - From Dusk til Dawn)



--
Cheers,

Paul






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Re: [gmx-users] secondary structure propensities of residues

[Mark Abraham]

On 10/08/2011 6:03 AM, César Ávila wrote:

Hi,
I downloaded release-4-5-patches from git. It compiles and installs 
successfully. Nevertheless I am getting a segmentation fault.


Are you using a version of DSSP that is compatible with GROMACS, pre 
previous discussion of DSSP changes?


Mark


With gdb I am getting the following messages


gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr 
-ssdump data.dat -b 17 -e 18 -dt 10

GNU gdb (GDB) 7.2-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 


This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Para las instrucciones de informe de errores, vea:
...
Leyendo símbolos desde /usr/local/gromacs/bin/do_dssp...(no se 
encontraron símbolos de depuración)hecho.

(gdb) run
Starting program: /usr/local/gromacs/bin/do_dssp -f ../0_trajout.xtc 
-s ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10

[Depuración de hilo usando libthread_db enabled]
 :-)  G  R  O  M  A  C  S  (-:

   Gromacs Runs One Microsecond At Cannonball Speeds

  :-)  VERSION 4.5.4-dev-20110803-e49fb5a  (-:

Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  /usr/local/gromacs/bin/do_dssp  (-:

Option Filename  Type Description

  -f ../0_trajout.xtc  InputTrajectory: xtc trr trj gro g96 
pdb cpt
  -s ../input/replica_0.tpr  InputStructure+mass(db): tpr tpb 
tpa gro

   g96 pdb
  -n  index.ndx  Input, Opt.  Index file
-ssdumpdata.dat  Output, Opt! Generic data file
-map ss.map  Input, Lib.  File that maps matrix data to colors
  -o ss.xpm  Output   X PixMap compatible matrix file
 -sc scount.xvg  Output   xvgr/xmgr file
  -a   area.xpm  Output, Opt. X PixMap compatible matrix file
 -tatotarea.xvg  Output, Opt. xvgr/xmgr file
 -aa   averarea.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-b   time   17  First frame (ps) to read from trajectory
-e   time   18  Last frame (ps) to read from trajectory
-dt  time   10  Only use frame when t MOD dt = first time (ps)
-tu  enum   ps  Time unit: fs, ps, ns, us, ms or s
-[no]w   bool   no  View output .xvg, .xpm, .eps and .pdb files
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-sss string HEBTSecondary structures for structure count

Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)
Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)

Program received signal SIGSEGV, Segmentation fault.
0x76ae043c in gmx_strcasecmp () from 
/usr/local/gromacs/lib/libgmx.so.6

(gdb) bt
#0  0x76ae043c in gmx_strcasecmp () from 
/usr/local/gromacs/lib/libgmx.so.6
#1  0x76ade68f in search_str () from 
/usr/local/gromacs/lib/libgmx.so.6
#2  0x77b508d4 in bPhobics () from 
/usr/local/gromacs/lib/libgmxana.so.6

#3  0x0040309a in main ()


2011/3/9 Mark Abraham >


On 10/03/2011 1:36 AM, Justin A. Lemkul wrote:



ZHAO Lina wrote:

Hi,

How do get the percentage of the secondary structure
propensities of residues?

seems dssp none such effect?


The scout.xvg file contains everything you need (in a broad
sense) - number of residues in a given secondary structure
over time.  If you need a per

[gmx-users] Topology for a new ligand

[Kavyashree M]

Dear gromacs users,

I wanted to know the steps to be followed
in order to generate a topology for a new
ligand. I went through the mailing list and
http://www.gromacs.org/Documentation/How-tos/Parameterization
but was not clear.

Awaiting your suggestions

Thanking you
With regards
M. Kavyashree
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Re: [gmx-users] Topology for a new ligand

[Justin A. Lemkul]

Kavyashree M wrote:

Dear gromacs users,

I wanted to know the steps to be followed
in order to generate a topology for a new
ligand. I went through the mailing list and
http://www.gromacs.org/Documentation/How-tos/Parameterization
but was not clear.



All force fields are different, and since you haven't said which one you're 
trying to use there's nothing that anyone can tell you.  Read the primary 
literature for the force field you want to use and follow the procedure laid out 
therein.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] pmf_calculation

[Justin A. Lemkul]

shahid nayeem wrote:

Dear Justin
I did some more sampling and sending you profile.xvg, histo.xvg. and 
hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell 
my the difference in profile.xvg and hist.xvg. Both should be same but I 
get different curves here.




I can't tell you the difference because you haven't shown how they were 
generated.  My blind guess is that hist.xvg (a very confusing name for a PMF 
profile) was generated from data that have poor sampling in two regions.  The 
contents of profile.xvg look normal.  I don't know which of these curves 
corresponds to histo.xvg, because the histograms therein look fine.


Please make sure to give full descriptions of these files.  You've quote a 
message that is over a month old.  I've replied to hundreds of messages since 
then and I do not remember the full context of our discussion.


-Justin

On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul > wrote:




shahid nayeem wrote:

Dear Justin
I did pmf calculation for my protein-protein complex using your
tutorial.Off course changing the pull_direction suitable for my
protein but more or less following the same strategy. I am using
gromacs_4.5.4 and g_wham utility. The profile.xvg file which I
get is attached and it shows two dips in PE curve. Please see it
and tell me why I am getting these dips.


You have insufficient sampling in at least these two regions.  Your
histograms should confirm this.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: A very good morning Sir

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not 
a private tutor.  I am CC'ing this message to the list and would ask that all 
further discussion be posted there.  Comments embedded below.


Sabitoj Singh Virk wrote:

Hello,
 
It could be really helpful of a person like you with  such high 
expertise to give me some insight in a problem i am facing while working 
in gromacs.Sir, I am trying to simulate a protein in buffer conditions ( 
Phosphate Buffer saline) whose conc. is : 137mM NaCl + 2.7 mM KCl + 
10.15 mM Na2HPo4 + 1.76 mM KH2Po4 . I have tried almost many ways to 
incorporate more than one salt in the solvent box but in vain. ' Genion 
' command does not work after one salt has been added (i.e only NaCl is 
added using -conc option and no other salt).If 'Genion' command is 
executed again,it shows : " No ions to add and no potential to calculate ".
 


The only way to build such a complex system is to manually specify the number of 
each ion or molecule to be added to the system.  Add your polyatomic ions first 
with genbox -ci -nmol, then solvate and add NaCl and KCl.  You will have to use 
the -np and -nn flags with genion.  A simple calculation based on the box volume 
will tell you how many ions to use.  Do not be surprised if you cannot get 
exactly the right concentration without using a horrendously large box.  Such 
small concentrations make it difficult to prepare the MD system exactly like the 
experiment and you may have to do a bit of rounding.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] pmf_calculation

[shahid nayeem]

I used following command
g_wham_4.5.4  -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
Both profile.xvg and hist.xvg are created with this command using same
pullf.xvg and .tpr files.
shahid Nayeem

On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> Dear Justin
>>
>> I did some more sampling and sending you profile.xvg, histo.xvg. and
>> hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg. please tell my
>> the difference in profile.xvg and hist.xvg. Both should be same but I get
>> different curves here.
>>
>>
> I can't tell you the difference because you haven't shown how they were
> generated.  My blind guess is that hist.xvg (a very confusing name for a PMF
> profile) was generated from data that have poor sampling in two regions.
>  The contents of profile.xvg look normal.  I don't know which of these
> curves corresponds to histo.xvg, because the histograms therein look fine.
>
> Please make sure to give full descriptions of these files.  You've quote a
> message that is over a month old.  I've replied to hundreds of messages
> since then and I do not remember the full context of our discussion.
>
> -Justin
>
>  On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear Justin
>>I did pmf calculation for my protein-protein complex using your
>>tutorial.Off course changing the pull_direction suitable for my
>>protein but more or less following the same strategy. I am using
>>gromacs_4.5.4 and g_wham utility. The profile.xvg file which I
>>get is attached and it shows two dips in PE curve. Please see it
>>and tell me why I am getting these dips.
>>
>>
>>You have insufficient sampling in at least these two regions.  Your
>>histograms should confirm this.
>>
>>-Justin
>>
>>-- ==**__==
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>
>> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>==**__==
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/Search
>>
>> >
>> before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>
>>Can't post? Read 
>> http://www.gromacs.org/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] pmf_calculation

[Justin A. Lemkul]

shahid nayeem wrote:

I used following command
g_wham_4.5.4  -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
Both profile.xvg and hist.xvg are created with this command using same 
pullf.xvg and .tpr files.


An identical command with identical input files producing totally different 
output?  Sorry, but I find that hard to believe.  Check your work and make sure 
you're using the input you think you are.  I suspect something's amiss and 
you're not seeing it.


-Justin


shahid Nayeem

On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul > wrote:




shahid nayeem wrote:

Dear Justin

I did some more sampling and sending you profile.xvg, histo.xvg.
and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg.
please tell my the difference in profile.xvg and hist.xvg. Both
should be same but I get different curves here.


I can't tell you the difference because you haven't shown how they
were generated.  My blind guess is that hist.xvg (a very confusing
name for a PMF profile) was generated from data that have poor
sampling in two regions.  The contents of profile.xvg look normal.
 I don't know which of these curves corresponds to histo.xvg,
because the histograms therein look fine.

Please make sure to give full descriptions of these files.  You've
quote a message that is over a month old.  I've replied to hundreds
of messages since then and I do not remember the full context of our
discussion.

-Justin

On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   shahid nayeem wrote:

   Dear Justin
   I did pmf calculation for my protein-protein complex
using your
   tutorial.Off course changing the pull_direction suitable
for my
   protein but more or less following the same strategy. I
am using
   gromacs_4.5.4 and g_wham utility. The profile.xvg file
which I
   get is attached and it shows two dips in PE curve. Please
see it
   and tell me why I am getting these dips.


   You have insufficient sampling in at least these two regions.
 Your
   histograms should confirm this.

   -Justin

   -- ====

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   MILES-IGERT Trainee
   Department of Biochemistry
   Virginia Tech
   Blacksburg, VA
   jalemkul[at]vt.edu   | (540)
231-9080

   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

   >

   ====
   -- gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users

   >
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search

   > before
posting!
   Please don't post (un)subscribe requests to the list. Use the www
   interface or send it to gmx-users-requ...@gromacs.org

   >.

   Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists

   >



-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
-- 
gmx-users mailing listgmx-users@gromacs.org


http://lists.gromacs.org/__mailman/listinfo/gmx-us

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Da-Wei Li]

Dear Mark and others

I did more tests and thought that it might come from numerical error. The
reasons are

1. If I use .trr file instead of the low precision xtc file, things become
better, ie, I get much less snapshots that has high energy.

2. I supplied -pforce in my mdrun -rerun and found that the high vdw energy
was usually caused by one pair of atoms, whose distance was just very near
the clash zone, so that small error on the coordinates would cause large
energy error. The force is always around 1.

3. Actually bond length and bond angle energies are also affected. I can
fully reproduce these two energies if I use .trr file in my rerun but will
get several tens of kj/mol error if I use .xtc file, for a protein of size
of 100 AA.


Now the question I still have is whether numerical error can be so large?
The xtc file has a precision of 0.001 nm. Anyway, I will test more by using
double precision Gromacs and define energy groups so that I can compare
energy of protein directly between original MD and rerun.



To Mark only

Thanks. Here it is my script for

 rerun:mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc nojump  (em.tpr
is generated for energy minimization, protein is in the middle of the box)

rerun .mdp file:

**

; Run parameters
integrator= md; leap-frog integrator
nsteps= 5000; 100 ns
dt= 0.002; 2 fs
; Output control
nstxout= 50; save coordinates every 1000 ps
nstvout= 50; save velocities every 1000 ps
nstxtcout= 5000; xtc compressed trajectory output every 1 ps
nstenergy= 5000; save energies every 1 ps
nstlog= 5000; update log file every 1 ps
xtc_grps= Protein; save protein part only
; Bond parameters
continuation= yes; Restarting after NPT
constraint_algorithm = lincs; holonomic constraints
constraints= hbonds; all bonds (even heavy atom-H bonds) constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cels
nstlist= 10; 20 fs
rlist= 0.8; short-range neighborlist cutoff (in nm)
rcoulomb= 0.8; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= cut-off; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= no; modified Berendsen thermostat
tc-grps= System; two coupling groups - more accurate
tau_t= 0.1; time constant, in ps
ref_t= 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl= no; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc= no; 3-D PBC
; Dispersion correction
;DispCorr= EnerPres; account for cut-off vdW scheme
DispCorr= no
; Velocity generation
gen_vel= no; Velocity generation is off



; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii   = 1
rgbradii = 0.8
gb_epsilon_solvent   = 80
gb_saltconc  = 0
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension   = 2.25936

***

Thanks all.

dawei
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Re: [gmx-users] pmf_calculation

[shahid nayeem]

Both files hist.xvg and profile.xvg both are simultaneous output of this
command. I did not run it twice, once to get profile.xvg and then to get
hist.xvg as you uderstood.

On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul  wrote:

>
>
> shahid nayeem wrote:
>
>> I used following command
>> g_wham_4.5.4  -it tpr-files.dat -if pullf-files.dat -o hist -unit kCal
>> Both profile.xvg and hist.xvg are created with this command using same
>> pullf.xvg and .tpr files.
>>
>
> An identical command with identical input files producing totally different
> output?  Sorry, but I find that hard to believe.  Check your work and make
> sure you're using the input you think you are.  I suspect something's amiss
> and you're not seeing it.
>
> -Justin
>
>  shahid Nayeem
>>
>>
>> On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>shahid nayeem wrote:
>>
>>Dear Justin
>>
>>I did some more sampling and sending you profile.xvg, histo.xvg.
>>and hist.xvg. I am sending histo.xvg hist.xvg and profile.xvg.
>>please tell my the difference in profile.xvg and hist.xvg. Both
>>should be same but I get different curves here.
>>
>>
>>I can't tell you the difference because you haven't shown how they
>>were generated.  My blind guess is that hist.xvg (a very confusing
>>name for a PMF profile) was generated from data that have poor
>>sampling in two regions.  The contents of profile.xvg look normal.
>> I don't know which of these curves corresponds to histo.xvg,
>>because the histograms therein look fine.
>>
>>Please make sure to give full descriptions of these files.  You've
>>quote a message that is over a month old.  I've replied to hundreds
>>of messages since then and I do not remember the full context of our
>>discussion.
>>
>>-Justin
>>
>>On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   shahid nayeem wrote:
>>
>>   Dear Justin
>>   I did pmf calculation for my protein-protein complex
>>using your
>>   tutorial.Off course changing the pull_direction suitable
>>for my
>>   protein but more or less following the same strategy. I
>>am using
>>   gromacs_4.5.4 and g_wham utility. The profile.xvg file
>>which I
>>   get is attached and it shows two dips in PE curve. Please
>>see it
>>   and tell me why I am getting these dips.
>>
>>
>>   You have insufficient sampling in at least these two regions.
>> Your
>>   histograms should confirm this.
>>
>>   -Justin
>>
>>   -- ==**==
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu   | (540)
>>
>>231-9080
>>
>>   http://www.bevanlab.biochem.__**__vt.edu/Pages/Personal/justin
>>
>> 
>> >
>>
>>   >
>> 
>> >>
>>
>>   ==**==
>>   -- gmx-users mailing listgmx-users@gromacs.org
>>
>>   **>
>>
>>
>>   
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>
>> 
>> >
>>   
>> 
>>
>> 
>> >>
>>   Please search the archive at
>>   
>> http://www.gromacs.org/**Support/Mailing_Lists/Search
>>
>> 
>> >
>>   
>> 
>>
>> >>
>> before
>>posting!
>>   Please don't post (un)subscribe requests to the list. Use the

Re: [gmx-users] pmf_calculation

[Justin A. Lemkul]

shahid nayeem wrote:
Both files hist.xvg and profile.xvg both are simultaneous output of this 
command. I did not run it twice, once to get profile.xvg and then to get 
hist.xvg as you uderstood.




They cannot be simultaneous output.  The file named "hist.xvg" contains a PMF 
profile and has a date stamp of July 5 (in the .xvg header).  The file 
"profile.xvg" is also a PMF profile and a has a date of August 11.  They were 
not produced simultaneously.  The file "histo.xvg" (with which you may be 
confusing "hist.xvg") was produced alongside "profile.xvg" and contains the 
umbrella sampling histograms, and was produced alongside "profile.xvg."


I think you've somehow lost track of which files are which.  It seems that 
"hist.xvg" contains the PMF profile from poor sampling, per our discussion a 
month ago, and "profile.xvg" contains something newer, likely with better data.


-Justin

On Thu, Aug 11, 2011 at 5:42 PM, Justin A. Lemkul > wrote:




shahid nayeem wrote:

I used following command
g_wham_4.5.4  -it tpr-files.dat -if pullf-files.dat -o hist
-unit kCal
Both profile.xvg and hist.xvg are created with this command
using same pullf.xvg and .tpr files.


An identical command with identical input files producing totally
different output?  Sorry, but I find that hard to believe.  Check
your work and make sure you're using the input you think you are.  I
suspect something's amiss and you're not seeing it.

-Justin

shahid Nayeem


On Thu, Aug 11, 2011 at 5:07 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   shahid nayeem wrote:

   Dear Justin

   I did some more sampling and sending you profile.xvg,
histo.xvg.
   and hist.xvg. I am sending histo.xvg hist.xvg and
profile.xvg.
   please tell my the difference in profile.xvg and
hist.xvg. Both
   should be same but I get different curves here.


   I can't tell you the difference because you haven't shown how
they
   were generated.  My blind guess is that hist.xvg (a very
confusing
   name for a PMF profile) was generated from data that have poor
   sampling in two regions.  The contents of profile.xvg look
normal.
I don't know which of these curves corresponds to histo.xvg,
   because the histograms therein look fine.

   Please make sure to give full descriptions of these files.
 You've
   quote a message that is over a month old.  I've replied to
hundreds
   of messages since then and I do not remember the full context
of our
   discussion.

   -Justin

   On Tue, Jul 5, 2011 at 5:16 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   
 
 | (540)

   231-9080

 
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


   >

 

 
 

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Justin A. Lemkul]

Da-Wei Li wrote:

Dear Mark and others

I did more tests and thought that it might come from numerical error. 
The reasons are


1. If I use .trr file instead of the low precision xtc file, things 
become better, ie, I get much less snapshots that has high energy.


2. I supplied -pforce in my mdrun -rerun and found that the high vdw 
energy was usually caused by one pair of atoms, whose distance was just 
very near the clash zone, so that small error on the coordinates would 
cause large energy error. The force is always around 1.


3. Actually bond length and bond angle energies are also affected. I can 
fully reproduce these two energies if I use .trr file in my rerun but 
will get several tens of kj/mol error if I use .xtc file, for a protein 
of size of 100 AA.



Now the question I still have is whether numerical error can be so 
large? The xtc file has a precision of 0.001 nm. Anyway, I will test 
more by using double precision Gromacs and define energy groups so that 
I can compare energy of protein directly between original MD and rerun.




To Mark only

Thanks. Here it is my script for

 rerun:mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc nojump  
(em.tpr is generated for energy minimization, protein is in the middle 
of the box)


rerun .mdp file:

**

; Run parameters
integrator= md; leap-frog integrator
nsteps= 5000; 100 ns
dt= 0.002; 2 fs
; Output control
nstxout= 50; save coordinates every 1000 ps
nstvout= 50; save velocities every 1000 ps
nstxtcout= 5000; xtc compressed trajectory output every 1 ps
nstenergy= 5000; save energies every 1 ps
nstlog= 5000; update log file every 1 ps
xtc_grps= Protein; save protein part only
; Bond parameters
continuation= yes; Restarting after NPT
constraint_algorithm = lincs; holonomic constraints
constraints= hbonds; all bonds (even heavy atom-H bonds) constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cels
nstlist= 10; 20 fs
rlist= 0.8; short-range neighborlist cutoff (in nm)
rcoulomb= 0.8; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= cut-off; Particle Mesh Ewald for long-range 
electrostatics

pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= no; modified Berendsen thermostat
tc-grps= System; two coupling groups - more accurate
tau_t= 0.1; time constant, in ps
ref_t= 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl= no; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc= no; 3-D PBC
; Dispersion correction
;DispCorr= EnerPres; account for cut-off vdW scheme
DispCorr= no
; Velocity generation
gen_vel= no; Velocity generation is off



; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii   = 1
rgbradii = 0.8
gb_epsilon_solvent   = 80
gb_saltconc  = 0
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension   = 2.25936

***

Thanks all.



Using cutoffs this small may be the source of your problem.  Proper implicit 
solvent calculations require longer cutoffs than would normally be used in 
explicit solvent MD.  Try with longer (2.0 nm) or infinite cutoffs and a fixed 
neighbor list (nstlist = 0) and see if that smooths out the problem.  What's 
likely happening now is that you've got interactions moving very quickly in and 
out of the very short cutoff, causing spikes in energy in between neighbor list 
updates.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

[chris . neale]

Dear Krapnik:

1. please make the test cases identical, that means doing a simulation  
that you may not really be interested in so that the solutes are the  
same for both lipid and octane. It also means setting the  
displacements to similar values in my opinion (because perhaps the  
problem is based on your box size along z and choice of pull_pbcatom  
for example). There is *something* strange happening, but let's  
eliminate all other possibilities before assuming that there is a  
problem with the source code.


2. Once you have a setup in which the only difference is octane vs.  
lipid (really the only difference please -- even add your octane  
pressure settings to the lipid simulation) and you find strange  
behaviour for octane and not lipid, then please attempt that same  
system with pull=umbrella in place of pull=constraints and see if the  
solute also drifts far from its initial position.


3. Your initial definition of the problem was a little misleading.  
Both Justin and I focused on third decimal place differences, but now  
you are saying that there is nm-scale motion along z. Please report  
those values for your test systems, which are outlined above, after  
you redo your tests with identical settings other than the switch from  
lipid to octane. -- I no longer thing that a double precision test is  
necessary if you are seeing nm-scale movement along z.


4. Perhaps I was a little hasty to complain about a bug-report style  
post. I did like all of the information that you provided. I just got  
the impression from your title and the end of your post that you  
thought it was a problem with gromacs (which it may still be) and I  
think that this is generally a counter-productive attitude because it  
hinders one from making the proper tests.


Chris

-- original message --

Re: Constraints not working in pull code (sometimes, sometimes not)
Krapnik krapnik at gmail.com
Thu Aug 11 09:53:24 CEST 2011

* Previous message: [gmx-users] append files in Gromacs 3.3
* Next message: [gmx-users] Constraints not working in pull code  
(sometimes, sometimes not)

* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Dear Justin
Thank you for your responses, but it still is not clear to me why is that
happening


I don't see any real problem here.  The DOPC membrane probably holds its

shape

better than the octanol slab and thus the reference position (which

determines

the constraint) is less mobile.


That is certain. When we were running free simulation, the box started to
narrow. Therefore we have frozen the box in xy plane.


As such, the constraint is more stable in DOPC
than in octanol.  The slight bump in the octanol system amounts to a

change of

0.16%, which I'd say is quite small.


The trouble is, that during next 10 ns the distance was between 2.0 - 4.0
and molecule moved outside of the ocatnol slab and inside, which is then
useless for calculation of PMF.


You're also looking at the first few
frames of the simulation, which may amount to equilibration, but you

haven't

mentioned if you've done anything prior to this run.


Previously, a free simulation with molecule on slab was run for 20 ns, from
which frame with small molecule at specidied depth was taken, so I suppose,
that the start is equilibrated.


As long as there is no systematic change in position, I'd say there's no

problem.

Unfortunately, there is as I have said before.

-Justin

Dear Chris,
thank you for responses as well.


I agree that Justin is probably correct, although constraints should
technically work just fine with a highly dynamic reference group. Any
problems should show up as the system blowing up, but not in correctly
setting the position.


I hope, that the position is set up ok, as it stays steady in DOPC.


I think that the problems can arise, however,
when you have multiple competing constraints. You might, for example,
try without constraining the octane bonds -- I think that you should
get perfect match in that case.


I will try.
The erroneous movement of molecule seems to be enhanced within XY-plane
frozen.
The curious thing is however, that when I did not constrain size of
xy-plane, then the distance to the COM of slab is not changing much (only
last digit changes), which in comparison to frozen XY-plane, where there is
huge movement above the slab and within is rather ok to me. Unfortunately, I
have the issue with narrowing of the box in the unconstrained XYplane
simulation, which also destroys any attempts for PMF as I have mentioned
before.


Also, it is worth comparing in single
and double precision.


I will try this either.


Still, I am not sure that you actually did a proper comparison for the
following 2 reasons:
1. you have apparently different masses for the pulled group:
Pull group 1:15 atoms, mass   194.194
Pull group 1:15 atoms, mass   146.146


The difference is not much in my opinion, while molecules tested are similar
in size and are run in

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Da-Wei Li]

Dear Justin

An implicit water simulaiton with this short cutoff is problematic but I
think it is fine for rerun. I want to exactly repeat the original energies
in the explicit water MD.

The manu say "neighbor list searching will be performed for every frame"
with rerun option. So that I don't think this is the cause.

best,

dawei

On Thu, Aug 11, 2011 at 8:47 AM, Justin A. Lemkul  wrote:

>
>
> Da-Wei Li wrote:
>
>> Dear Mark and others
>>
>> I did more tests and thought that it might come from numerical error. The
>> reasons are
>>
>> 1. If I use .trr file instead of the low precision xtc file, things become
>> better, ie, I get much less snapshots that has high energy.
>>
>> 2. I supplied -pforce in my mdrun -rerun and found that the high vdw
>> energy was usually caused by one pair of atoms, whose distance was just very
>> near the clash zone, so that small error on the coordinates would cause
>> large energy error. The force is always around 1.
>>
>> 3. Actually bond length and bond angle energies are also affected. I can
>> fully reproduce these two energies if I use .trr file in my rerun but will
>> get several tens of kj/mol error if I use .xtc file, for a protein of size
>> of 100 AA.
>>
>>
>> Now the question I still have is whether numerical error can be so large?
>> The xtc file has a precision of 0.001 nm. Anyway, I will test more by using
>> double precision Gromacs and define energy groups so that I can compare
>> energy of protein directly between original MD and rerun.
>>
>>
>>
>> To Mark only
>>
>> Thanks. Here it is my script for
>>
>>  rerun:mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
>> superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc nojump
>>  (em.tpr is generated for energy minimization, protein is in the middle of
>> the box)
>>
>> rerun .mdp file:
>>
>> 
>>
>> ; Run parameters
>> integrator= md; leap-frog integrator
>> nsteps= 5000; 100 ns
>> dt= 0.002; 2 fs
>> ; Output control
>> nstxout= 50; save coordinates every 1000 ps
>> nstvout= 50; save velocities every 1000 ps
>> nstxtcout= 5000; xtc compressed trajectory output every 1 ps
>> nstenergy= 5000; save energies every 1 ps
>> nstlog= 5000; update log file every 1 ps
>> xtc_grps= Protein; save protein part only
>> ; Bond parameters
>> continuation= yes; Restarting after NPT
>> constraint_algorithm = lincs; holonomic constraints
>> constraints= hbonds; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter= 1; accuracy of LINCS
>> lincs_order= 4; also related to accuracy
>> ; Neighborsearching
>> ns_type= grid; search neighboring grid cels
>> nstlist= 10; 20 fs
>> rlist= 0.8; short-range neighborlist cutoff (in nm)
>> rcoulomb= 0.8; short-range electrostatic cutoff (in nm)
>> rvdw= 1.0; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype= cut-off; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order= 4; cubic interpolation
>> fourierspacing= 0.12; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl= no; modified Berendsen thermostat
>> tc-grps= System; two coupling groups - more accurate
>> tau_t= 0.1; time constant, in ps
>> ref_t= 300 ; reference temperature, one for each group, in
>> K
>> ; Pressure coupling is on
>> pcoupl= no; Pressure coupling on in NPT
>> pcoupltype= isotropic; uniform scaling of box vectors
>> tau_p= 2.0; time constant, in ps
>> ref_p= 1.0; reference pressure, in bar
>> compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
>> ; Periodic boundary conditions
>> pbc= no; 3-D PBC
>> ; Dispersion correction
>> ;DispCorr= EnerPres; account for cut-off vdW scheme
>> DispCorr= no
>> ; Velocity generation
>> gen_vel= no; Velocity generation is off
>>
>>
>>
>> ; IMPLICIT SOLVENT ALGORITHM
>> implicit_solvent = GBSA
>> gb_algorithm = OBC
>> nstgbradii   = 1
>> rgbradii = 0.8
>> gb_epsilon_solvent   = 80
>> gb_saltconc  = 0
>> gb_obc_alpha = 1
>> gb_obc_beta  = 0.8
>> gb_obc_gamma = 4.85
>> gb_dielectric_offset = 0.009
>> sa_algorithm = Ace-approximation
>> sa_surface_tension   = 2.25936
>>
>> 
>> ***
>>
>> Thanks all.
>>
>>
> Using cutoffs this small may be the source of your problem.  Proper
> implicit solvent calculations require longer cutoffs than would normally be
> used in explicit solvent MD.  Try with longer (

[gmx-users] Re: VMD_PLUGIN_PATH

[PAUL NEWMAN]

Dear Mark,

Thanks for replying. Yes I am using bash. Yes the bash recognize the set
path. When I do echo, I got the follwoing

echo $VMD_PLUGIN_PATH

/home/pet/vmd/1.9/plugins/molfile

What can be wrong? Maybe the program is not in this folder? Which program is
searching for this pluging

Thanks for your help.


-- Forwarded message --
From: Mark Abraham 
To: Discussion list for GROMACS users 
Date: Thu, 11 Aug 2011 19:51:04 +1000
Subject: Re: [gmx-users] VMD_PLUGIN_PATH
On 10/08/2011 1:21 PM, PAUL NEWMAN wrote:

Hi Gromacs Users,

I am using the gromacs analysing tools to analyze my DCD file produced by
NAMD. I set up the VMD_PLUGIN_PATH before running however I got the error
that the VMD_PLUGIN_PATH was not set up. Can anyone give me a hand? Please
see below the details. Thanks for the help

export VMD_PLUGIN_PATH=/home/pet/vmd/1.9/plugins/molfile


Are you using a shell where this works? What does "echo $VMD_PLUGIN_PATH"
say afterwards?

Mark


g_gyrate_d -f protein.dcd -s ../IN/protein.pdb

##

##

The file format of protein.dcd is not a known trajectory format to GROMACS.
Please make sure that the file is a trajectory!
GROMACS will now assume it to be a trajectory and will try to open it using
the VMD plug-ins.
This will only work in case the VMD plugins are found and it is a trajectory
format supported by VMD.

No VMD Plugins found
Set the environment variable VMD_PLUGIN_PATH to the molfile folder within
the
VMD installation.
The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to match.

---
Program g_gyrate_d, VERSION 4.5.3
Source code file: trxio.c, line: 867

Fatal error:
Not supported in read_first_frame: protein.dcd
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Lets Kill the Fucking Band"  (Tom Savini - From Dusk til Dawn)



-- 
Cheers,

Paul



-- 
Cheers,

Paul
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Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Justin A. Lemkul]

Da-Wei Li wrote:

Dear Justin

An implicit water simulaiton with this short cutoff is problematic but I 
think it is fine for rerun. I want to exactly repeat the original 
energies in the explicit water MD.


The manu say "neighbor list searching will be performed for every frame" 
with rerun option. So that I don't think this is the cause.




Right, forgot about that.  I still think the cutoffs are a problem, though.

-Justin


best,

dawei

On Thu, Aug 11, 2011 at 8:47 AM, Justin A. Lemkul > wrote:




Da-Wei Li wrote:

Dear Mark and others

I did more tests and thought that it might come from numerical
error. The reasons are

1. If I use .trr file instead of the low precision xtc file,
things become better, ie, I get much less snapshots that has
high energy.

2. I supplied -pforce in my mdrun -rerun and found that the high
vdw energy was usually caused by one pair of atoms, whose
distance was just very near the clash zone, so that small error
on the coordinates would cause large energy error. The force is
always around 1.

3. Actually bond length and bond angle energies are also
affected. I can fully reproduce these two energies if I use .trr
file in my rerun but will get several tens of kj/mol error if I
use .xtc file, for a protein of size of 100 AA.


Now the question I still have is whether numerical error can be
so large? The xtc file has a precision of 0.001 nm. Anyway, I
will test more by using double precision Gromacs and define
energy groups so that I can compare energy of protein directly
between original MD and rerun.



To Mark only

Thanks. Here it is my script for

 rerun:mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc
nojump  (em.tpr is generated for energy minimization, protein is
in the middle of the box)

rerun .mdp file:

**__

; Run parameters
integrator= md; leap-frog integrator
nsteps= 5000; 100 ns
dt= 0.002; 2 fs
; Output control
nstxout= 50; save coordinates every 1000 ps
nstvout= 50; save velocities every 1000 ps
nstxtcout= 5000; xtc compressed trajectory output
every 1 ps
nstenergy= 5000; save energies every 1 ps
nstlog= 5000; update log file every 1 ps
xtc_grps= Protein; save protein part only
; Bond parameters
continuation= yes; Restarting after NPT
constraint_algorithm = lincs; holonomic constraints
constraints= hbonds; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cels
nstlist= 10; 20 fs
rlist= 0.8; short-range neighborlist cutoff (in nm)
rcoulomb= 0.8; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= cut-off; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= no; modified Berendsen thermostat
tc-grps= System; two coupling groups - more accurate
tau_t= 0.1; time constant, in ps
ref_t= 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl= no; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
; Periodic boundary conditions
pbc= no; 3-D PBC
; Dispersion correction
;DispCorr= EnerPres; account for cut-off vdW scheme
DispCorr= no
; Velocity generation
gen_vel= no; Velocity generation is off



; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii   = 1
rgbradii = 0.8
gb_epsilon_solvent   = 80
gb_saltconc  = 0

[gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

[Micholas Smith]

(My apologizes for the double post, my mail client apparently sent my previous 
email as html, so here is a clean re-print)

Hello,

After undergoing a fresh installation of Gromacs 4.5.4, I still can't 
seem to get the mdrun-gpu program to compile and install. In order to 
get the original package to install I had to use the standard autoconf/make 
method (cmake kept getting stuck at the 'make' phase).

I have managed to get an older binary version of the mdrun-gpu working 
correctly, but I would like to not have two different of versions of 
gromacs floating around my office.

The current output from the cmake gives:


cmake ../ -DGMX_OPENMM=ON -DGMX_THREADS=OFF

-- Using default binary suffix: "-gpu"

-- Using default library suffix: "_gpu"

-- checking for module 'libxml-2.0'

--   package 'libxml-2.0' not found

-- Could NOT find LibXml2  (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)

CMake Error at 
/usr/share/cmake-2.6/Modules/FindPackageHandleStandardArgs.cmake:57 (MESSAGE):

  Could NOT find CUDA (missing: CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)

Call Stack (most recent call first):

  cmake/FindCUDA.cmake:690 (find_package_handle_standard_args)

  CMakeLists.txt:434 (find_package)

---



Any ideas on a fix? Or does anyone knows of a means to compile mdrun-gpu using 
the standard autoconf/make method?



Thanks in advance.



Smitty
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[gmx-users] How to install FFTW 3.2.2

[afsaneh maleki]

Hi,

To compile a single-precision version of the libraries and install FFTW
version 3.2.

I followed the steps inhttp://
www.gromacs.org/Downloads/Installation_Instructions#Prerequisites .

my  computer characteristics:
Root at …fftw-3.2.2]# uname -a
Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7
21:25:57 EST 2009 i686 i686 i386 GNU/Linux

I used the following command:
Root at …fftw-3.2.2]# ./configure --enable-threads --enable-float
--enable-sse
Root at …fftw-3.2.2]make

I get these errors:

make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'
make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'
Making all in m4
make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4'
make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2'

I used "make distclean" and try to configure again with.


Root at …fftw-3.2.2]#./configure --enable-threads --enable-float
--enable-sse --disable-shared


Root at …fftw-3.2.2]#./configure --enable-threads --enable-float
--enable-sse --enable-shared


Root at …fftw-3.2.2]#./configure --enable-threads --enable-float
--enable-sse --with-pic

Root at …fftw-3.2.2]#./configure --enable-threads --enable-float
--enable-shared
Root at …fftw-3.2.2]#./configure --enable-threads --enable-float --with-pic

I get the same errors during FFTW version 3.2.2 compilation (the "make"
step) as above.

What commands are useful for compiling FFTW version 3.2.2 on my computer?


Thanks in advance,
Afsaneh
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Re: [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

[Justin A. Lemkul]

Micholas Smith wrote:

(My apologizes for the double post, my mail client apparently sent my previous 
email as html, so here is a clean re-print)

Hello,

After undergoing a fresh installation of Gromacs 4.5.4, I still can't 
seem to get the mdrun-gpu program to compile and install. In order to 
get the original package to install I had to use the standard autoconf/make 
method (cmake kept getting stuck at the 'make' phase).


I have managed to get an older binary version of the mdrun-gpu working 
correctly, but I would like to not have two different of versions of 
gromacs floating around my office.


The current output from the cmake gives:


cmake ../ -DGMX_OPENMM=ON -DGMX_THREADS=OFF

-- Using default binary suffix: "-gpu"

-- Using default library suffix: "_gpu"

-- checking for module 'libxml-2.0'

--   package 'libxml-2.0' not found

-- Could NOT find LibXml2  (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)

CMake Error at 
/usr/share/cmake-2.6/Modules/FindPackageHandleStandardArgs.cmake:57 (MESSAGE):

  Could NOT find CUDA (missing: CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)

Call Stack (most recent call first):

  cmake/FindCUDA.cmake:690 (find_package_handle_standard_args)

  CMakeLists.txt:434 (find_package)

---



Any ideas on a fix? Or does anyone knows of a means to compile mdrun-gpu using 
the standard autoconf/make method?



Compiling mdrun-gpu requires cmake.  It looks like the build mechanism can't 
find the require CUDA implementation.  If your headers and libraries are in a 
nonstandard location, you'll have to set the two mentioned variables 
appropriately so that cmake can find them.


-Justin




Thanks in advance.



Smitty


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Please search the archive at 
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Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Da-Wei Li]

Dear Justin

You are right about the cut-off. The vdw energy spike disappeared after I
increased the cut-off in the rerun. But I still don't understand why? Can
the cutoff error build up to several thousand kj/mol for 100AA protein.

Again I would like to emphasize NOT to use a xtc file in MM/PBSA type
calculation. The error is just too large.

best,

dawei

On Thu, Aug 11, 2011 at 9:03 AM, Justin A. Lemkul  wrote:

>
>
> Da-Wei Li wrote:
>
>> Dear Justin
>>
>> An implicit water simulaiton with this short cutoff is problematic but I
>> think it is fine for rerun. I want to exactly repeat the original energies
>> in the explicit water MD.
>>
>> The manu say "neighbor list searching will be performed for every frame"
>> with rerun option. So that I don't think this is the cause.
>>
>>
> Right, forgot about that.  I still think the cutoffs are a problem, though.
>
> -Justin
>
>  best,
>>
>> dawei
>>
>>
>> On Thu, Aug 11, 2011 at 8:47 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Da-Wei Li wrote:
>>
>>Dear Mark and others
>>
>>I did more tests and thought that it might come from numerical
>>error. The reasons are
>>
>>1. If I use .trr file instead of the low precision xtc file,
>>things become better, ie, I get much less snapshots that has
>>high energy.
>>
>>2. I supplied -pforce in my mdrun -rerun and found that the high
>>vdw energy was usually caused by one pair of atoms, whose
>>distance was just very near the clash zone, so that small error
>>on the coordinates would cause large energy error. The force is
>>always around 1.
>>
>>3. Actually bond length and bond angle energies are also
>>affected. I can fully reproduce these two energies if I use .trr
>>file in my rerun but will get several tens of kj/mol error if I
>>use .xtc file, for a protein of size of 100 AA.
>>
>>
>>Now the question I still have is whether numerical error can be
>>so large? The xtc file has a precision of 0.001 nm. Anyway, I
>>will test more by using double precision Gromacs and define
>>energy groups so that I can compare energy of protein directly
>>between original MD and rerun.
>>
>>
>>
>>To Mark only
>>
>>Thanks. Here it is my script for
>>
>> rerun:mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
>>superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc
>>nojump  (em.tpr is generated for energy minimization, protein is
>>in the middle of the box)
>>
>>rerun .mdp file:
>>
>>__
>>
>>; Run parameters
>>integrator= md; leap-frog integrator
>>nsteps= 5000; 100 ns
>>dt= 0.002; 2 fs
>>; Output control
>>nstxout= 50; save coordinates every 1000 ps
>>nstvout= 50; save velocities every 1000 ps
>>nstxtcout= 5000; xtc compressed trajectory output
>>every 1 ps
>>nstenergy= 5000; save energies every 1 ps
>>nstlog= 5000; update log file every 1 ps
>>xtc_grps= Protein; save protein part only
>>; Bond parameters
>>continuation= yes; Restarting after NPT
>>constraint_algorithm = lincs; holonomic constraints
>>constraints= hbonds; all bonds (even heavy atom-H bonds)
>>constrained
>>lincs_iter= 1; accuracy of LINCS
>>lincs_order= 4; also related to accuracy
>>; Neighborsearching
>>ns_type= grid; search neighboring grid cels
>>nstlist= 10; 20 fs
>>rlist= 0.8; short-range neighborlist cutoff (in nm)
>>rcoulomb= 0.8; short-range electrostatic cutoff (in nm)
>>rvdw= 1.0; short-range van der Waals cutoff (in nm)
>>; Electrostatics
>>coulombtype= cut-off; Particle Mesh Ewald for long-range
>>electrostatics
>>pme_order= 4; cubic interpolation
>>fourierspacing= 0.12; grid spacing for FFT
>>; Temperature coupling is on
>>tcoupl= no; modified Berendsen thermostat
>>tc-grps= System; two coupling groups - more accurate
>>tau_t= 0.1; time constant, in ps
>>ref_t= 300 ; reference temperature, one for each
>>group, in K
>>; Pressure coupling is on
>>pcoupl= no; Pressure coupling on in NPT
>>pcoupltype= isotropic; uniform scaling of box vectors
>>tau_p= 2.0; time constant, in ps
>>ref_p= 1.0; reference pressure, in bar
>>compressibili

Re: [gmx-users] How to install FFTW 3.2.2

[Justin A. Lemkul]

afsaneh maleki wrote:

Hi,
 
To compile a single-precision version of the libraries and install FFTW 
version 3.2.
 
I followed the steps 
inhttp://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites 
 .
 
my  computer characteristics:

Root at …fftw-3.2.2]# uname -a
Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7 
21:25:57 EST 2009 i686 i686 i386 GNU/Linux
 
I used the following command:
Root at …fftw-3.2.2]# ./configure --enable-threads --enable-float 
--enable-sse

Root at …fftw-3.2.2]make
 
I get these errors:
 
make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'

make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'
Making all in m4
make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4'
make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2'
 


These are not errors.  These statements are normal.


I used "make distclean" and try to configure again with.
 
 
Root at …fftw-3.2.2]#./configure --enable-threads --enable-float 
--enable-sse --disable-shared
 
 
Root at …fftw-3.2.2]#./configure --enable-threads --enable-float 
--enable-sse --enable-shared
 
 
Root at …fftw-3.2.2]#./configure --enable-threads --enable-float 
--enable-sse --with-pic
 
Root at …fftw-3.2.2]#./configure --enable-threads --enable-float 
--enable-shared

Root at …fftw-3.2.2]#./configure --enable-threads --enable-float --with-pic
 
I get the same errors during FFTW version 3.2.2 compilation (the "make" 
step) as above.
 
What commands are useful for compiling FFTW version 3.2.2 on my computer?




Try again from the start with your original command.  It looks like it worked 
fine.  If you get an error, it will actually print "error" to the terminal.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

[Андрей Гончар]

Hi!
Maybe you have to install a missing packages, libxml2 and CUDA?

2011/8/11 Micholas Smith :
> (My apologizes for the double post, my mail client apparently sent my 
> previous email as html, so here is a clean re-print)
>
> Hello,
>
> After undergoing a fresh installation of Gromacs 4.5.4, I still can't
> seem to get the mdrun-gpu program to compile and install. In order to
> get the original package to install I had to use the standard autoconf/make
> method (cmake kept getting stuck at the 'make' phase).
>
> I have managed to get an older binary version of the mdrun-gpu working
> correctly, but I would like to not have two different of versions of
> gromacs floating around my office.
>
> The current output from the cmake gives:
>
>
> cmake ../ -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>
> -- Using default binary suffix: "-gpu"
>
> -- Using default library suffix: "_gpu"
>
> -- checking for module 'libxml-2.0'
>
> --   package 'libxml-2.0' not found
>
> -- Could NOT find LibXml2  (missing:  LIBXML2_LIBRARIES LIBXML2_INCLUDE_DIR)
>
> CMake Error at 
> /usr/share/cmake-2.6/Modules/FindPackageHandleStandardArgs.cmake:57 (MESSAGE):
>
>   Could NOT find CUDA (missing: CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
>
> Call Stack (most recent call first):
>
>   cmake/FindCUDA.cmake:690 (find_package_handle_standard_args)
>
>   CMakeLists.txt:434 (find_package)
>
> ---
>
>
>
> Any ideas on a fix? Or does anyone knows of a means to compile mdrun-gpu 
> using the standard autoconf/make method?
>
>
>
> Thanks in advance.
>
>
>
> Smitty
> --
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[gmx-users] Regarding parametrisation

[Ravi Kumar Venkatraman]

Dear Justin,
 I was reading one of your literature on building
GROMOS-compatible small molecule topologies. I was trying to reproduce the
AM1BCC partial charges for the p-cresol using Antechamber from amber tools
version 1.5.

I will enlist what I have got and with literature values and gromos96
values. I am getting somewhat close to that but I dont know whether it is
right or wrong?

CH3 AM1BCC  Literature AM1BCCGROMOS 96
C   0.0764-0.0487
H1 0.0004 0.0399
H2 0.0044 0.0437
H3 0.0044 0.0437
sum   0.0856 0.0786  0.

CH Aromatic
C  -0.1383-0.1381 -0.1000
H   0.1368 0.1371  0.1000

C-CH3
C   -0.1196-0.1123 0.

COH
C   0.1642  0.1187 0.1500
O  -0.7452 -0.4987-0.5480
H   0.6190  0.4179 0.3980

Thank you.

Ravi Kumar V
IPC Dept.,
IISC, INDIA.
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Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Mark Abraham]

On 11/08/2011 10:22 PM, Da-Wei Li wrote:

Dear Mark and others

I did more tests and thought that it might come from numerical error. 
The reasons are


1. If I use .trr file instead of the low precision xtc file, things 
become better, ie, I get much less snapshots that has high energy.


That doesn't make sense if the underlying frames are the same in your 
.xtc and .trr files. However, if you're talking about different numbers 
of frames, then you probably have transient periodicity artefacts.




2. I supplied -pforce in my mdrun -rerun and found that the high vdw 
energy was usually caused by one pair of atoms, whose distance was 
just very near the clash zone, so that small error on the coordinates 
would cause large energy error. The force is always around 1.


Sounds like you have a non-equilibrium trajectory (from your EM?), in 
which case small deviations can have large effects.




3. Actually bond length and bond angle energies are also affected. I 
can fully reproduce these two energies if I use .trr file in my rerun 
but will get several tens of kj/mol error if I use .xtc file, for a 
protein of size of 100 AA.


Several tens of kJ/mol error in the non-bonded energy looks OK compared 
to the magnitude of the non-bonded energy. Anyway, if your purpose is to 
compare energies computed from the same configurations, then you should 
use the same configurations for computing the energies, not 
approximations to those configurations.





Now the question I still have is whether numerical error can be so 
large? The xtc file has a precision of 0.001 nm. Anyway, I will test 
more by using double precision Gromacs and define energy groups so 
that I can compare energy of protein directly between original MD and 
rerun.




To Mark only

Thanks. Here it is my script for

 rerun:mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc nojump  
(em.tpr is generated for energy minimization, protein is in the middle 
of the box)


Here you are generating a nojump trajectory file, but you are not doing 
your rerun on it. That could explain some symptoms - you might not have 
whole molecules.


Mark



rerun .mdp file:

**

; Run parameters
integrator= md; leap-frog integrator
nsteps= 5000; 100 ns
dt= 0.002; 2 fs
; Output control
nstxout= 50; save coordinates every 1000 ps
nstvout= 50; save velocities every 1000 ps
nstxtcout= 5000; xtc compressed trajectory output every 1 ps
nstenergy= 5000; save energies every 1 ps
nstlog= 5000; update log file every 1 ps
xtc_grps= Protein; save protein part only
; Bond parameters
continuation= yes; Restarting after NPT
constraint_algorithm = lincs; holonomic constraints
constraints= hbonds; all bonds (even heavy atom-H bonds) 
constrained

lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
ns_type= grid; search neighboring grid cels
nstlist= 10; 20 fs
rlist= 0.8; short-range neighborlist cutoff (in nm)
rcoulomb= 0.8; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype= cut-off; Particle Mesh Ewald for long-range 
electrostatics

pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= no; modified Berendsen thermostat
tc-grps= System; two coupling groups - more accurate
tau_t= 0.1; time constant, in ps
ref_t= 300 ; reference temperature, one for each 
group, in K

; Pressure coupling is on
pcoupl= no; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 2.0; time constant, in ps
ref_p= 1.0; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc= no; 3-D PBC
; Dispersion correction
;DispCorr= EnerPres; account for cut-off vdW scheme
DispCorr= no
; Velocity generation
gen_vel= no; Velocity generation is off



; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii   = 1
rgbradii = 0.8
gb_epsilon_solvent   = 80
gb_saltconc  = 0
gb_obc_alpha = 1
gb_obc_beta  = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension   = 2.25936

***

Thanks all.

dawei











-- 
gmx-

Re: [gmx-users] Re: VMD_PLUGIN_PATH

[Mark Abraham]

On 11/08/2011 11:02 PM, PAUL NEWMAN wrote:

Dear Mark,

Thanks for replying. Yes I am using bash. Yes the bash recognize the 
set path. When I do echo, I got the follwoing


echo $VMD_PLUGIN_PATH

/home/pet/vmd/1.9/plugins/molfile

What can be wrong? Maybe the program is not in this folder? Which 
program is searching for this pluging


Perhaps there is some mismatch in how GROMACS and VMD were compiled, but 
I have no idea how to diagnose that.


Mark



Thanks for your help.


-- Forwarded message --
From: Mark Abraham >
To: Discussion list for GROMACS users >

Date: Thu, 11 Aug 2011 19:51:04 +1000
Subject: Re: [gmx-users] VMD_PLUGIN_PATH
On 10/08/2011 1:21 PM, PAUL NEWMAN wrote:

Hi Gromacs Users,

I am using the gromacs analysing tools to analyze my DCD file 
produced by NAMD. I set up the VMD_PLUGIN_PATH before running however 
I got the error that the VMD_PLUGIN_PATH was not set up. Can anyone 
give me a hand? Please see below the details. Thanks for the help


export VMD_PLUGIN_PATH=/home/pet/vmd/1.9/plugins/molfile


Are you using a shell where this works? What does "echo 
$VMD_PLUGIN_PATH" say afterwards?


Mark


g_gyrate_d -f protein.dcd -s ../IN/protein.pdb

##

##

The file format of protein.dcd is not a known trajectory format to 
GROMACS.

Please make sure that the file is a trajectory!
GROMACS will now assume it to be a trajectory and will try to open it 
using the VMD plug-ins.
This will only work in case the VMD plugins are found and it is a 
trajectory format supported by VMD.


No VMD Plugins found
Set the environment variable VMD_PLUGIN_PATH to the molfile folder 
within the

VMD installation.
The architecture (e.g. 32bit versus 64bit) of Gromacs and VMD has to 
match.


---
Program g_gyrate_d, VERSION 4.5.3
Source code file: trxio.c, line: 867

Fatal error:
Not supported in read_first_frame: protein.dcd
For more information and tips for troubleshooting, please check the 
GROMACS

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

"Lets Kill the Fucking Band"  (Tom Savini - From Dusk til Dawn)



--
Cheers,

Paul



--
Cheers,

Paul






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[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

[intra\sa175950]

Dear All,

 

Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing list
a very useful tutorial [1] to scale the Coulombic 1-4 interactions when we
combine forcefields with different fudgeLJ and fudgeQQ values. I am trying
to apply this trick to a system containing a peptide and a micelle simulated
with AMBER99SB-ILDN and GLYCAM force fields, respectively (see my previous
message [2]). 

 

I have followed all the steps described in [2] and computed the sigma_ij and
epsilon_ij values for the peptide and the micelle with comb_rules 2 (i.e.
sigma_ij=1/2(sigma_i+sigma_j) and epsilon_ij=sqrt(epsilon_i*epsilon_j). The
epsilon_i and sigma_i are taken from the [ atomtypes ] section in the
ffnonbonded.itp file

 

However, in the step 3 in [2], it is said that the peptide the pair
interaction values (i.e. epsilon) should be divided by 10 and these
"values/12" include in the pairtypes section. I suspect a typo here. Indeed,
if I set the general fudgeLJ and fudgeQQ to 1.0 and 0.166, I should have
a ratio of 10 (for (0.8/(0.16)))*1/2 for epsilon_ij and not "12". Am
I right?

 

To test the changes, I have performed three nsteps=0 runs in NVT ensemble
for a simple system (1 peptide and 1 glycolipid solvated in water) with the
initial and modified and non-modified nonbonded parameters:

 

1- With ffnonbbonded.itp file non-modified with fudgeLJ=0.5 and
fudgeQQ=0.8   --- > peptide

2- With ffnonbbonded.itp file non-modified with fudgeLJ=1.0 and fudgeQQ=1.0
--- >  micelle

3- With ffnonbbonded.itp file modified with fudgeLJ=1.0 and
fudgeQQ=0.166  --- >  all

 

and compared the *.trr files obtained from these the three runs. 

 

The only differences I found are, indeed, in the force section of the *.trr
files for atoms involved in the modified pair section. To be sure that my
modifications are corrects, I would like to obtain the individual pair
energy values of the micelle and the peptide. How to obtain this values?   

 

[1] http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html

[2] http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html

 

Thank you again for your help and advices.  

 

Stephane

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[gmx-users] Re: -dt option in g_velacc

[Jinan Niu]

On 8/08/2011 11:08 PM, Mark Abraham wrote:

>I don't quite follow your question, but for correlation functions to be
>computed accurately, you need data collected much more frequently >than
>the relevant time scales. That can require good planning.
>Mark

Hi,Mark and other gmx users：
when I used g_velacc to calculate VAF,  I found the range of frequency of the 
power spectrum is related with dt, so if is there is some solutions? can the 
complication of gmx by double decision solve it?

--

Sincerely yours 
Dr Ji-Nan Niu 
School of Materials Science and Engineering.
China University of Mining and Technology.
Jiangsu Province, XuZhou 221116
P. R. China
_
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Re: [gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

[Mark Abraham]

On 12/08/2011 12:16 AM, intra\sa175950 wrote:


Dear All,

Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing 
list a very useful tutorial [1] to scale the Coulombic 1-4 
interactions when we combine forcefields with different fudgeLJ and 
fudgeQQ values. I am trying to apply this trick to a system containing 
a peptide and a micelle simulated with AMBER99SB-ILDN and GLYCAM force 
fields, respectively (see my previous message [2]).


I have followed all the steps described in [2] and computed the 
sigma_ij and epsilon_ij values for the peptide and the micelle with 
comb_rules 2 (i.e. sigma_ij=1/2(sigma_i+sigma_j) and 
epsilon_ij=sqrt(epsilon_i*epsilon_j). The epsilon_i and sigma_i are 
taken from the [ atomtypes ] section in the ffnonbonded.itp file


However, in the step 3 in [2], it is said that the peptide the pair 
interaction values (i.e. epsilon) should be divided by 10 and these 
"values/12" include in the pairtypes section. I suspect a typo here. 
Indeed, if I set the general fudgeLJ and fudgeQQ to 1.0 and 0.166, 
I should have a ratio of 10 (for (0.8/(0.16)))*1/2 for 
epsilon_ij and not "12". Am I right?


To test the changes, I have performed three nsteps=0 runs in NVT 
ensemble for a simple system (1 peptide and 1 glycolipid solvated in 
water) with the initial and modified and non-modified nonbonded 
parameters:


1- With ffnonbbonded.itp file non-modified with fudgeLJ=0.5 and 
fudgeQQ=0.8   --- > peptide


2- With ffnonbbonded.itp file non-modified with fudgeLJ=1.0 and 
fudgeQQ=1.0  --- >  micelle


3- With ffnonbbonded.itp file modified with fudgeLJ=1.0 and 
fudgeQQ=0.166  --- >  all




Using mdrun -rerun allows you to compare more than one configuration in 
a run, and avoid any issues associated with bond constraints and 
neighbour lists.



and compared the *.trr files obtained from these the three runs.

The only differences I found are, indeed, in the force section of the 
*.trr files for atoms involved in the modified pair section. To be 
sure that my modifications are corrects, I would like to obtain the 
individual pair energy values of the micelle and the peptide. How to 
obtain this values?




Use grompp -pp, and selectively zero out charges and/or VDW parameters 
for appropriate [moleculetypes] in the reruns.


Mark

[1] 
http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html


[2] http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html

Thank you again for your help and advices.

Stephane





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Re: [gmx-users] strange vdw energy from rerun with GBSA model.

[Da-Wei Li]

Hello

Please see my response below.

On Thu, Aug 11, 2011 at 10:23 AM, Mark Abraham wrote:

>  On 11/08/2011 10:22 PM, Da-Wei Li wrote:
>
> Dear Mark and others
>
> I did more tests and thought that it might come from numerical error. The
> reasons are
>
> 1. If I use .trr file instead of the low precision xtc file, things become
> better, ie, I get much less snapshots that has high energy.
>
>
> That doesn't make sense if the underlying frames are the same in your .xtc
> and .trr files. However, if you're talking about different numbers of
> frames, then you probably have transient periodicity artefacts.
>


They are the same but different precision. I used a mdp file without PBC. I
believe this is reasonable because I can fully reproduce the bond length and
angle energy if I use trr file but cannot reproduce if I use .xtc file.


>
> 2. I supplied -pforce in my mdrun -rerun and found that the high vdw energy
> was usually caused by one pair of atoms, whose distance was just very near
> the clash zone, so that small error on the coordinates would cause large
> energy error. The force is always around 1.
>
>
> Sounds like you have a non-equilibrium trajectory (from your EM?), in which
> case small deviations can have large effects.
>


No. It is from a stable NPT trajectory with explicit water models. The
forces are around 1 but are not larger.


>
>
>
> 3. Actually bond length and bond angle energies are also affected. I can
> fully reproduce these two energies if I use .trr file in my rerun but will
> get several tens of kj/mol error if I use .xtc file, for a protein of size
> of 100 AA.
>
>
> Several tens of kJ/mol error in the non-bonded energy looks OK compared to
> the magnitude of the non-bonded energy. Anyway, if your purpose is to
> compare energies computed from the same configurations, then you should use
> the same configurations for computing the energies, not approximations to
> those configurations.
>
>

That is why I say precesion in xtc file is not enough for bond length, angle
potential and vdw potential.


>
>
> Now the question I still have is whether numerical error can be so large?
> The xtc file has a precision of 0.001 nm. Anyway, I will test more by using
> double precision Gromacs and define energy groups so that I can compare
> energy of protein directly between original MD and rerun
>
>
As Justin suggested, increase cutoff in rerun can remove the vdw energy
spike.




>
> To Mark only
>
> Thanks. Here it is my script for
>
>  rerun:mdrun -v -s pbsa.tpr -rerun coor.xtc -e rerun
> superpose:  trjconv -s em.tpr -f coor.xtc -o nojump.xtc -pbc nojump
> (em.tpr is generated for energy minimization, protein is in the middle of
> the box)
>
>
> Here you are generating a nojump trajectory file, but you are not doing
> your rerun on it. That could explain some symptoms - you might not have
> whole molecules.
>
>
I am very sorry for this typo. I do use the nojump.xtc in my rerun.



>  Mark
>
>
>
> rerun .mdp file:
>
> **
>
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 5000; 100 ns
> dt= 0.002; 2 fs
> ; Output control
> nstxout= 50; save coordinates every 1000 ps
> nstvout= 50; save velocities every 1000 ps
> nstxtcout= 5000; xtc compressed trajectory output every 1 ps
> nstenergy= 5000; save energies every 1 ps
> nstlog= 5000; update log file every 1 ps
> xtc_grps= Protein; save protein part only
> ; Bond parameters
> continuation= yes; Restarting after NPT
> constraint_algorithm = lincs; holonomic constraints
> constraints= hbonds; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter= 1; accuracy of LINCS
> lincs_order= 4; also related to accuracy
> ; Neighborsearching
> ns_type= grid; search neighboring grid cels
> nstlist= 10; 20 fs
> rlist= 0.8; short-range neighborlist cutoff (in nm)
> rcoulomb= 0.8; short-range electrostatic cutoff (in nm)
> rvdw= 1.0; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype= cut-off; Particle Mesh Ewald for long-range
> electrostatics
> pme_order= 4; cubic interpolation
> fourierspacing= 0.12; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl= no; modified Berendsen thermostat
> tc-grps= System; two coupling groups - more accurate
> tau_t= 0.1; time constant, in ps
> ref_t= 300 ; reference temperature, one for each group, in
> K
> ; Pressure coupling is on
> pcoupl= no; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box vectors
> tau_p= 2.0; time constant, in ps
> ref_p= 1.0; reference pressure, in bar
> 

[gmx-users] how to calculate the conc in the genion

[lina]

Hi,

after using genion -conc 0.1

certain number of Na and Cl were added in solvent.

but when I tried to calculate back, namely, based on the number of Na
and Cl, the number of water molecular and the box volumn,
but seems can't come back, I mean, can't obtain the result of 0.1mol/L.

I read the manual, "...the specified concentration as computed from
the volume of the cell..."

the cell? Has anyone tried to calculate the concentration back?

( I guess might the way I calculate was wrong? the Avogadro's Constant
= 6.0221415 × 10^23 mol-1)


Thanks with best regards,

lina
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[gmx-users] How to install gromacs 4.5.1

[afsaneh maleki]

Hi,


My characteristics computer:



Root at …fftw-3.2.2]# uname -a

Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7
21:25:57 EST 2009 i686 i686 i386 GNU/Linux



To install FFTW version 3.2.2.

I used the following commands:

Root at …fftw-3.2.2]#  ./configure --enable-threads --enable-float
--enable-shared

  Root at …fftw-3.2.2]#  make

  Root at …fftw-3.2.2]#  make install

After using “make” and “make install”, it get me the following text at end:

make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'

make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'

Making all in m4

make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4'

make[2]: Nothing to be done for `all'.

make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4'

make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2'



..

To install gromacs version 4.5.1

root@localhost gromacs-4.5.1]#./configure

* On most platforms you can save 10X space with dynamic libraries, although

  the binaries might be less portable. Why not try --enable-shared ?



[root@localhost gromacs-4.5.1]#make

[root@localhost gromacs-4.5.1]#make install

[root@localhost gromacs-4.5.1]# make links

cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \

for i in $programs; do \

   (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0);
\

done



when i used each command with” –h” or “–help” I obtain the followinf error:

[afsaneh@localhost ~]$ g_analyze -h

g_analyze: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory



[afsaneh@localhost ~]$ editconf -h

editconf: error while loading shared libraries: libfftw3f.so.3: cannot open
shared object file: No such file or directory



How to solve this problem?



Best wishes,

Afsaneh
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Re: [gmx-users] Re: -dt option in g_velacc

[Mark Abraham]

On 12/08/2011 12:30 AM, Jinan Niu wrote:

On 8/08/2011 11:08 PM, Mark Abraham wrote:

>I don't quite follow your question, but for correlation functions to be
>computed accurately, you need data collected much more frequently >than
>the relevant time scales. That can require good planning.
>Mark
Hi,Mark and other gmx users:
when I used g_velacc to calculate VAF,  I found the range of frequency 
of the power spectrum is related with dt, so if is there is some 
solutions? can the complication of gmx by double decision solve it?


If the value for g_velacc -dt is comparable to the correlation time 
scale of the system, then the results of an analysis will be sensitive 
to that value. In such cases, you need to use the smallest possible -dt 
value (i.e. omit the value) and/or collect data more frequently.


Mark
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Re: [gmx-users] how to calculate the conc in the genion

[Mark Abraham]

On 12/08/2011 12:37 AM, lina wrote:

Hi,

after using genion -conc 0.1

certain number of Na and Cl were added in solvent.

but when I tried to calculate back, namely, based on the number of Na
and Cl, the number of water molecular and the box volumn,
but seems can't come back, I mean, can't obtain the result of 0.1mol/L.

I read the manual, "...the specified concentration as computed from
the volume of the cell..."

the cell? Has anyone tried to calculate the concentration back?

( I guess might the way I calculate was wrong? the Avogadro's Constant
= 6.0221415 × 10^23 mol-1)


I'd be amazed if the error was in the code and not in your calculation. 
The number of water molecules doesn't matter for the calculation of the 
ion concentration, of course. Pay attention to your box shape. And do 
consider the number of ions has to be an integer, so for a given volume 
you cannot get arbitrarily close to a given concentration.


Mark
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Re: [gmx-users] How to install gromacs 4.5.1

[Mark Abraham]

On 12/08/2011 12:38 AM, afsaneh maleki wrote:

Hi,


My characteristics computer:

Root at ...fftw-3.2.2]# uname -a

Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 
7 21:25:57 EST 2009 i686 i686 i386 GNU/Linux


To install FFTW version 3.2.2.

I used the following commands:

Root at ...fftw-3.2.2]#./configure --enable-threads --enable-float 
--enable-shared


Root at ...fftw-3.2.2]#make

Root at ...fftw-3.2.2]#make install

After using "make" and "make install", it get me the following text at 
end:


make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'

make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'

Making all in m4

make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4'

make[2]: Nothing to be done for `all'.

make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4'

make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2'

..

To install gromacs version 4.5.1

root@localhost gromacs-4.5.1]#./configure



You aren't configuring to use fftw3. You should probably use the same 
--enable-shared setting for both FFTW and GROMACS.


* On most platforms you can save 10X space with dynamic libraries, 
although


the binaries might be less portable. Why not try --enable-shared ?

[root@localhost gromacs-4.5.1]#make

[root@localhost gromacs-4.5.1]#make install

[root@localhost gromacs-4.5.1]# make links

cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \

for i in $programs; do \

(test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \

done

when i used each command with" --h" or "--help" I obtain the followinf 
error:


[afsaneh@localhost ~]$ g_analyze -h

g_analyze: error while loading shared libraries: libfftw3f.so.3: 
cannot open shared object file: No such file or directory




Sounds like somehow the make environment could find the FFTW libraries, 
but the execution environment could not. Do heed the advice here 
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation 
(and the rest of the instructions, too)


Mark


[afsaneh@localhost ~]$ editconf -h

editconf: error while loading shared libraries: libfftw3f.so.3: cannot 
open shared object file: No such file or directory


How to solve this problem?

Best wishes,

Afsaneh





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[gmx-users] vsites with NAC and opls

[chris . neale]

This is fixed, just posting for posterity.

If one wants to run pdb2gmx with -vsites hydrogens on gromacs 4.5.4 or  
4.0.7 while using the oplss ff, there is the error message:


Fatal error:
Can't find dummy mass for type opls_242 bonded to type opls_238 in the  
virtual site database (.vsd files). Add it to the database!


To fix this, one must then add the following line:

   opls_242  opls_238   MCH3A

to the [ CH3 ] section of oplsaa.ff/aminoacids.vsd

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Re: [gmx-users] How to install gromacs 4.5.1

[lina]

cd /usr/lib

(or locate libfftw3.so.3.2.4)

you may notice the /usr/lib/libfftw3.so.3.2.4

make a link,
sudo ln -sf /usr/lib/libfftw3.so.3.2.4 /usr/lib/libfftw3.so.3

then shall be no problem.


On Thu, Aug 11, 2011 at 10:50 PM, Mark Abraham  wrote:
> On 12/08/2011 12:38 AM, afsaneh maleki wrote:
>
> Hi,
>
> My characteristics computer:
>
>
>
> Root at …fftw-3.2.2]# uname -a
>
> Linux localhost.localdomain 2.6.31.5-127.fc12.i686.PAE #1 SMP Sat Nov 7
> 21:25:57 EST 2009 i686 i686 i386 GNU/Linux
>
>
>
> To install FFTW version 3.2.2.
>
> I used the following commands:
>
> Root at …fftw-3.2.2]#  ./configure --enable-threads --enable-float
> --enable-shared
>
>   Root at …fftw-3.2.2]#  make
>
>   Root at …fftw-3.2.2]#  make install
>
> After using “make” and “make install”, it get me the following text at end:
>
> make[3]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'
>
> make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/tools'
>
> Making all in m4
>
> make[2]: Entering directory `/home/afsaneh/m/fftw-3.2.2/m4'
>
> make[2]: Nothing to be done for `all'.
>
> make[2]: Leaving directory `/home/afsaneh/m/fftw-3.2.2/m4'
>
> make[1]: Leaving directory `/home/afsaneh/m/fftw-3.2.2'
>
>
>
> ..
>
> To install gromacs version 4.5.1
>
> root@localhost gromacs-4.5.1]#./configure
>
> You aren't configuring to use fftw3. You should probably use the same
> --enable-shared setting for both FFTW and GROMACS.
>
> * On most platforms you can save 10X space with dynamic libraries, although
>
>   the binaries might be less portable. Why not try --enable-shared ?
>
>
>
> [root@localhost gromacs-4.5.1]#make
>
> [root@localhost gromacs-4.5.1]#make install
>
> [root@localhost gromacs-4.5.1]# make links
>
> cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
>
>     for i in $programs; do \
>
>        (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0);
> \
>
>     done
>
>
>
> when i used each command with” –h” or “–help” I obtain the followinf error:
>
> [afsaneh@localhost ~]$ g_analyze -h
>
> g_analyze: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
> Sounds like somehow the make environment could find the FFTW libraries, but
> the execution environment could not. Do heed the advice here
> http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation
> (and the rest of the instructions, too)
>
> Mark
>
>
>
> [afsaneh@localhost ~]$ editconf -h
>
> editconf: error while loading shared libraries: libfftw3f.so.3: cannot open
> shared object file: No such file or directory
>
>
>
> How to solve this problem?
>
>
>
> Best wishes,
>
> Afsaneh
>
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Best Regards,

lina
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[gmx-users] PCA and Free energy landscape

[bipin singh]

Hello,
I have done PCA using cartesian coordinates by the help of
gromacs(g_covar and g_anaeig),
then using the 2-d projection of trajectory on first two eigenvectors
as reaction coordinates,I have calculated a 2-d representation of the
gibbs free energy landscape(g_sham) using gromacs.Now
on this landscape I want to map the conformations(structures from the
MD trajectories)
of the protein onto the different region(for eg:minima)of this landscape.
Please suggest how can I perform this task

-- 
---
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Re: [gmx-users] how to calculate the conc in the genion

[lina]

On Thu, Aug 11, 2011 at 10:41 PM, Mark Abraham  wrote:
> On 12/08/2011 12:37 AM, lina wrote:
>>
>> Hi,
>>
>> after using genion -conc 0.1
>>
>> certain number of Na and Cl were added in solvent.
>>
>> but when I tried to calculate back, namely, based on the number of Na
>> and Cl, the number of water molecular and the box volumn,
>> but seems can't come back, I mean, can't obtain the result of 0.1mol/L.
>>
>> I read the manual, "...the specified concentration as computed from
>> the volume of the cell..."
>>
>> the cell? Has anyone tried to calculate the concentration back?
>>
>> ( I guess might the way I calculate was wrong? the Avogadro's Constant
>> = 6.0221415 в 10^23 mol-1)
>
> I'd be amazed if the error was in the code and not in your calculation. The
> number of water molecules doesn't matter for the calculation of the ion
> concentration, of course. Pay attention to your box shape. And do consider
> the number of ions has to be an integer, so for a given volume you cannot
> get arbitrarily close to a given concentration.

I did use the box volumn first, but a bit far away from it.

so I wonder whether it means the concentration of the solvent involved,

another concern, what if the cell has large area no water, so how the
concentration calculated, still the whole box?

Thanks,
>
> Mark
> --
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>



-- 
Best Regards,

lina
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[gmx-users] reg genion

[vidhya sankar]

Dear justin,
  Thank you for your previous mail
  I am using genion pro gramme  if i use genion programme 
using random option in number of times Then will it add positive and negative 
ions in  different (xyz) coordinate in every time
otherwise will it show same coordinate in every time for all ions ? i want to 
clarify 
i am expecting your  reply 
Thanks in advance 
 
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[gmx-users] RE: gmx-users Digest, Vol 88, Issue 65

[intra\sa175950]

Thank Mark, I will try your suggestions. 

Stephane

Message: 4
Date: Fri, 12 Aug 2011 00:31:46 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] Use different fudgeLJ and fudgeQQ values in
simulations with the AMBER force field
To: Discussion list for GROMACS users 
Message-ID: <4e43e7d2.6050...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

On 12/08/2011 12:16 AM, intra\sa175950 wrote:
>
> Dear All,
>
> Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing 
> list a very useful tutorial [1] to scale the Coulombic 1-4 
> interactions when we combine forcefields with different fudgeLJ and 
> fudgeQQ values. I am trying to apply this trick to a system containing 
> a peptide and a micelle simulated with AMBER99SB-ILDN and GLYCAM force 
> fields, respectively (see my previous message [2]).
>
> I have followed all the steps described in [2] and computed the 
> sigma_ij and epsilon_ij values for the peptide and the micelle with 
> comb_rules 2 (i.e. sigma_ij=1/2(sigma_i+sigma_j) and 
> epsilon_ij=sqrt(epsilon_i*epsilon_j). The epsilon_i and sigma_i are 
> taken from the [ atomtypes ] section in the ffnonbonded.itp file
>
> However, in the step 3 in [2], it is said that the peptide the pair 
> interaction values (i.e. epsilon) should be divided by 10 and these 
> "values/12" include in the pairtypes section. I suspect a typo here. 
> Indeed, if I set the general fudgeLJ and fudgeQQ to 1.0 and 0.166, 
> I should have a ratio of 10 (for (0.8/(0.16)))*1/2 for 
> epsilon_ij and not "12". Am I right?
>
> To test the changes, I have performed three nsteps=0 runs in NVT 
> ensemble for a simple system (1 peptide and 1 glycolipid solvated in 
> water) with the initial and modified and non-modified nonbonded 
> parameters:
>
> 1- With ffnonbbonded.itp file non-modified with fudgeLJ=0.5 and 
> fudgeQQ=0.8   --- > peptide
>
> 2- With ffnonbbonded.itp file non-modified with fudgeLJ=1.0 and 
> fudgeQQ=1.0  --- >  micelle
>
> 3- With ffnonbbonded.itp file modified with fudgeLJ=1.0 and 
> fudgeQQ=0.166  --- >  all
>

Using mdrun -rerun allows you to compare more than one configuration in 
a run, and avoid any issues associated with bond constraints and 
neighbour lists.

> and compared the *.trr files obtained from these the three runs.
>
> The only differences I found are, indeed, in the force section of the 
> *.trr files for atoms involved in the modified pair section. To be 
> sure that my modifications are corrects, I would like to obtain the 
> individual pair energy values of the micelle and the peptide. How to 
> obtain this values?
>

Use grompp -pp, and selectively zero out charges and/or VDW parameters 
for appropriate [moleculetypes] in the reruns.

Mark

> [1] 
> http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html
>
> [2] http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html
>
> Thank you again for your help and advices.
>
> Stephane
>
>
>

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End of gmx-users Digest, Vol 88, Issue 65
*


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Re: [gmx-users] how to calculate the conc in the genion

[Tsjerk Wassenaar]

Hi,

>> I'd be amazed if the error was in the code and not in your calculation. The
>> number of water molecules doesn't matter for the calculation of the ion
>> concentration, of course. Pay attention to your box shape. And do consider
>> the number of ions has to be an integer, so for a given volume you cannot
>> get arbitrarily close to a given concentration.

The error is, to my humble opinion, in the reasoning. Concentration is
a macroscopic property, and when dealing with a minute volume, the
concentration of something in it is ill defined. Especially when
there's something else in that volume, taking up a significant amount
of space, like a membrane, protein or void, it becomes troublesome. I
would argue that the worst you can do in that case is take the volume
of the box and calculate the number of things to add from there to
reach a given concentration.
Whether the number of water molecules matters for the calculation of
the ion concentration depends on the unit you use for concentration.
Probably  molality is a better option than molarity. For that you do
take the number of water molecules. Frankly, that's what I usually do.
Doing so will give a desired concentration of ions in the solvent,
regardless of volume occupied by other (big) solutes or by nothing.
There is just one problem that stays nonetheless; in how far does the
bulk concentration you use as target correspond to the local
concentration you might need to use? Solutes, membranes and voids may
alter the local concentration significantly.

By the way, Lina, it would have helped if you had given the equations,
numbers and outcomes that lead you to believe there is something
wrong.

Hope it helps,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] how to calculate the conc in the genion

[lina]

On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar  wrote:
> Hi,
>
>>> I'd be amazed if the error was in the code and not in your calculation. The
>>> number of water molecules doesn't matter for the calculation of the ion
>>> concentration, of course. Pay attention to your box shape. And do consider
>>> the number of ions has to be an integer, so for a given volume you cannot
>>> get arbitrarily close to a given concentration.
>
> The error is, to my humble opinion, in the reasoning. Concentration is
> a macroscopic property, and when dealing with a minute volume, the
> concentration of something in it is ill defined. Especially when
> there's something else in that volume, taking up a significant amount
> of space, like a membrane, protein or void, it becomes troublesome. I
> would argue that the worst you can do in that case is take the volume
> of the box and calculate the number of things to add from there to
> reach a given concentration.
> Whether the number of water molecules matters for the calculation of
> the ion concentration depends on the unit you use for concentration.
> Probably  molality is a better option than molarity. For that you do
> take the number of water molecules. Frankly, that's what I usually do.
> Doing so will give a desired concentration of ions in the solvent,
> regardless of volume occupied by other (big) solutes or by nothing.
> There is just one problem that stays nonetheless; in how far does the
> bulk concentration you use as target correspond to the local
> concentration you might need to use? Solutes, membranes and voids may
> alter the local concentration significantly.
>
> By the way, Lina, it would have helped if you had given the equations,
> numbers and outcomes that lead you to believe there is something
> wrong.

I did another quick check, which regardless of my way of calculation.

two cubic box, the same conc.
I compared the ratio of  Na+CL in two box  is 24/60=0.4
while I compared the volumn ratio is 149.6/533.39=0.28.

This way is easily for others to check too. read the ions from two
topol.top and the dimension from two .gro.

>
> Hope it helps,

Thanks,
>
> Tsjerk
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Best Regards,

lina
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Re: [gmx-users] Topology for a new ligand

[Kavyashree M]

Dear users,

I was mentioning about OPLSAA force field for ATP
and other small molecule.  I just wanted to know the
procedure to be followed and some guidance from
people who have created topologies for such
molecules manually. I am going through chapter 5 of
the manual. But wanted some useful suggestions.

Thank you
With Regards
M. Kavyashree


On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul  wrote:

>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>
>> I wanted to know the steps to be followed
>> in order to generate a topology for a new
>> ligand. I went through the mailing list and
>> http://www.gromacs.org/**Documentation/How-tos/**Parameterization
>> but was not clear.
>>
>>
> All force fields are different, and since you haven't said which one you're
> trying to use there's nothing that anyone can tell you.  Read the primary
> literature for the force field you want to use and follow the procedure laid
> out therein.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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Re: [gmx-users] how to calculate the conc in the genion

[lina]

On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar  wrote:
> Hi,
>
>>> I'd be amazed if the error was in the code and not in your calculation. The
>>> number of water molecules doesn't matter for the calculation of the ion
>>> concentration, of course. Pay attention to your box shape. And do consider
>>> the number of ions has to be an integer, so for a given volume you cannot
>>> get arbitrarily close to a given concentration.
>
> The error is, to my humble opinion, in the reasoning. Concentration is
> a macroscopic property, and when dealing with a minute volume, the
> concentration of something in it is ill defined. Especially when
> there's something else in that volume, taking up a significant amount
> of space, like a membrane, protein or void, it becomes troublesome. I
> would argue that the worst you can do in that case is take the volume
> of the box and calculate the number of things to add from there to
> reach a given concentration.
> Whether the number of water molecules matters for the calculation of
> the ion concentration depends on the unit you use for concentration.
> Probably  molality is a better option than molarity. For that you do
> take the number of water molecules. Frankly, that's what I usually do.
> Doing so will give a desired concentration of ions in the solvent,
> regardless of volume occupied by other (big) solutes or by nothing.
> There is just one problem that stays nonetheless; in how far does the
> bulk concentration you use as target correspond to the local
> concentration you might need to use? Solutes, membranes and voids may
> alter the local concentration significantly.
>

Yes. I do agree with you.

Here I have a field problem, I will be very glad if I can be told
which part of calculation is wrong.

a cubic box: Volumn = 101.57 *105.03 * 87.82 A  = 9.369E-25  m^3 = 93.69E-23 L
total ions: 121

so the concentration based on the box volume is:

121/AvagadroConstant/Volumn =
121/6.022E23/93.69E-23=121/6.022/9.369=0.214 mol/L?

But before when I used -conc, the number I chose maybe 0.1 or 0.15
mol/L, but not 0.2mol/L.

Here if consider the water, certainly the water volumn will be greatly
smaller than the box volumn, so the concentration will reach very
high?

I might be wrong in some way, hope someone can point out.

Thanks,

> By the way, Lina, it would have helped if you had given the equations,
> numbers and outcomes that lead you to believe there is something
> wrong.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users@gromacs.org
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>



-- 
Best Regards,

lina
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Re: [gmx-users] how to calculate the conc in the genion

[Justin A. Lemkul]

Tsjerk Wassenaar wrote:

Hi,


I'd be amazed if the error was in the code and not in your calculation. The
number of water molecules doesn't matter for the calculation of the ion
concentration, of course. Pay attention to your box shape. And do consider
the number of ions has to be an integer, so for a given volume you cannot
get arbitrarily close to a given concentration.


The error is, to my humble opinion, in the reasoning. Concentration is
a macroscopic property, and when dealing with a minute volume, the
concentration of something in it is ill defined. Especially when
there's something else in that volume, taking up a significant amount
of space, like a membrane, protein or void, it becomes troublesome. I
would argue that the worst you can do in that case is take the volume
of the box and calculate the number of things to add from there to
reach a given concentration.


I'm wondering if you can elaborate a bit on this.  I can understand your point 
in the case of interfacial systems, membranes, or other biphasic systems, but 
for a protein in water, why does the volume occupied by the protein matter?  All 
components - protein, water, ions - are all part of the same phase and 
contribute to the total volume.  Experimentally, one simply adds the desired 
amount (either dry or from concentrated stock) and dilutes to the necessary 
final volume.  There is no distinction made for volume occupied by a protein, 
substrate, or buffer component.  Is this distinction really necessary in the 
simple case of a protein in water?  I'd be curious to hear your thoughts.


-Justin


Whether the number of water molecules matters for the calculation of
the ion concentration depends on the unit you use for concentration.
Probably  molality is a better option than molarity. For that you do
take the number of water molecules. Frankly, that's what I usually do.
Doing so will give a desired concentration of ions in the solvent,
regardless of volume occupied by other (big) solutes or by nothing.
There is just one problem that stays nonetheless; in how far does the
bulk concentration you use as target correspond to the local
concentration you might need to use? Solutes, membranes and voids may
alter the local concentration significantly.

By the way, Lina, it would have helped if you had given the equations,
numbers and outcomes that lead you to believe there is something
wrong.

Hope it helps,

Tsjerk





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Regarding parametrisation

[Justin A. Lemkul]

Ravi Kumar Venkatraman wrote:

Dear Justin,
 I was reading one of your literature on building 
GROMOS-compatible small molecule topologies. I was trying to reproduce 
the AM1BCC partial charges for the p-cresol using Antechamber from amber 
tools version 1.5.




This is a newer version than what we used in that paper (we used 1.0), so there 
may be some differences.  I understand there have been some tweaks to the QM 
programs.


I will enlist what I have got and with literature values and gromos96 
values. I am getting somewhat close to that but I dont know whether it 
is right or wrong?




With a different version, you may not achieve exactly what we did.  Nothing 
looks "wrong" here, per se.  Note that, as we conclude in the paper, none of the 
tested QM methods produce "correct" charges; all needed to be modified based on 
Gromos96 parameterization methodology (fitting to condensed-phase criteria).


-Justin


CH3 AM1BCC  Literature AM1BCCGROMOS 96
C   0.0764-0.0487 
H1 0.0004 0.0399

H2 0.0044 0.0437
H3 0.0044 0.0437
sum   0.0856 0.0786  0.

CH Aromatic
C  -0.1383-0.1381 -0.1000
H   0.1368 0.1371  0.1000

C-CH3
C   -0.1196-0.1123 0.

COH
C   0.1642  0.1187 0.1500
O  -0.7452 -0.4987-0.5480
H   0.6190  0.4179 0.3980

Thank you.

Ravi Kumar V
IPC Dept.,
IISC, INDIA.





















--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] reg genion

[Justin A. Lemkul]

vidhya sankar wrote:

Dear justin,
  Thank you for your previous mail
  I am using genion pro gramme  if i use genion 
programme using random option in number of times Then will it add 
positive and negative ions in  different (xyz) coordinate in every time
otherwise will it show same coordinate in every time for all ions ? i 
want to clarify


To get different positions, set a different value of -seed.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Topology for a new ligand

[Justin A. Lemkul]

Kavyashree M wrote:

Dear users,

I was mentioning about OPLSAA force field for ATP
and other small molecule.  I just wanted to know the
procedure to be followed and some guidance from
people who have created topologies for such
molecules manually. I am going through chapter 5 of
the manual. But wanted some useful suggestions.



Methods for parameterizing molecules for OPLS-AA are described in fairly 
extensive detail in the 2001 OPLS-AA paper cited in the manual.  The manual 
itself will only tell you how to implement parameters in Gromacs, not how to 
derive them.


-Justin


Thank you
With Regards
M. Kavyashree


On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Dear gromacs users,

I wanted to know the steps to be followed
in order to generate a topology for a new
ligand. I went through the mailing list and
http://www.gromacs.org/__Documentation/How-tos/__Parameterization

but was not clear.


All force fields are different, and since you haven't said which one
you're trying to use there's nothing that anyone can tell you.  Read
the primary literature for the force field you want to use and
follow the procedure laid out therein.

-Justin

-- 
==__==


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


==__==
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] how to calculate the conc in the genion

[Tsjerk Wassenaar]

Hey Justin,

> I'm wondering if you can elaborate a bit on this.  I can understand your
> point in the case of interfacial systems, membranes, or other biphasic
> systems, but for a protein in water, why does the volume occupied by the
> protein matter?  All components - protein, water, ions - are all part of the
> same phase and contribute to the total volume.  Experimentally, one simply
> adds the desired amount (either dry or from concentrated stock) and dilutes
> to the necessary final volume.  There is no distinction made for volume
> occupied by a protein, substrate, or buffer component.  Is this distinction
> really necessary in the simple case of a protein in water?  I'd be curious
> to hear your thoughts.

The protein will be solved in some solution that has a specified
amount of salt, as well as other stuff. That solution thus has a
specific water to salt ratio. Let's assume there is no specific
interaction between protein and salt, then in the vicinity of the
protein there will be the same ratio of water to salt. If you cut out
a small portion, containing the protein, and warp opposite ends so as
to make it periodic, there should still be that same water to salt
ratio. The volume of the protein is not suddenly also occupied by some
ions. Vice versa, mimicking such a solution in silico is best done by
adding ions up to the water to ion ratio that corresponds to the
concentration of the medium. Of course, if you consider the whole
system, the protein will have an insignificant effect on the volume
and the distinction between molarity and molality won't matter much.
But if you cut out a piece of about the scale of the protein, then it
will make a difference. Note that interactions between the protein and
the salt will mess things up, but you can't really say a priori in
which way.

I'd be happy to hear further arguments of the contrary though :)

Cheers,

Tsjerk

>
> -Justin
>
>> Whether the number of water molecules matters for the calculation of
>> the ion concentration depends on the unit you use for concentration.
>> Probably  molality is a better option than molarity. For that you do
>> take the number of water molecules. Frankly, that's what I usually do.
>> Doing so will give a desired concentration of ions in the solvent,
>> regardless of volume occupied by other (big) solutes or by nothing.
>> There is just one problem that stays nonetheless; in how far does the
>> bulk concentration you use as target correspond to the local
>> concentration you might need to use? Solutes, membranes and voids may
>> alter the local concentration significantly.
>>
>> By the way, Lina, it would have helped if you had given the equations,
>> numbers and outcomes that lead you to believe there is something
>> wrong.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] compile template.c

[Park, Jae Hyun nmn]

Dear GMX users,

Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3.
As a first test, when I run "make" in the directory of "template" I got the 
following message:

--
cc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
-funroll-all-loops -std=gnu99 -pthread -I./include  -I/usr/include/libxml2 
-I/home/h1y/gromacs-4.5.3s/include-I/home/h1y/fftw3s/include  -c -o work.o 
work.c

cc  -L/home/h1y/gromacs-4.5.3s/lib -L/home/h1y/fftw3s/lib   -o work work.o -lmd 
-lgmx -lfftw3f -lxml2  -lnsl -lm

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x6): In function 
`vmddlopen':

: undefined reference to `dlopen'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x11): In function 
`vmddlerror':

: undefined reference to `dlerror'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x21): In function 
`vmddlsym':

: undefined reference to `dlsym'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x31): In function 
`vmddlclose':

: undefined reference to `dlclose'

collect2: ld returned 1 exit status

make: *** [work] Error 1


I would deeply appreciate if any help why I got those erros and how to figure 
out.

Best regards,
Jae H. Park


===
Jae Hyun Park, Ph.D.
Physics Division
Oak Ridge National Laboratory
P.O. Box 2008, MS-6372
Oak Ridge, TN 37831
Phone (865) 241-1482
E-mail pa...@ornl.gov--
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[gmx-users] compile template.c

[Park, Jae Hyun nmn]

Dear GMX users,

Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3.
As a first test, when I run "make" in the directory of "template" I got the 
following message:

--
cc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
-funroll-all-loops -std=gnu99 -pthread -I./include  -I/usr/include/libxml2 
-I/home/h1y/gromacs-4.5.3s/include-I/home/h1y/fftw3s/include  -c -o work.o 
work.c

cc  -L/home/h1y/gromacs-4.5.3s/lib -L/home/h1y/fftw3s/lib   -o work work.o -lmd 
-lgmx -lfftw3f -lxml2  -lnsl -lm

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x6): In function 
`vmddlopen':

: undefined reference to `dlopen'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x11): In function 
`vmddlerror':

: undefined reference to `dlerror'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x21): In function 
`vmddlsym':

: undefined reference to `dlsym'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x31): In function 
`vmddlclose':

: undefined reference to `dlclose'

collect2: ld returned 1 exit status

make: *** [work] Error 1


I would deeply appreciate if any help why I got those erros and how to figure 
out.

Best regards,
Jae H. Park


===
Jae Hyun Park, Ph.D.
Physics Division
Oak Ridge National Laboratory
P.O. Box 2008, MS-6372
Oak Ridge, TN 37831
Phone (865) 241-1482
E-mail pa...@ornl.gov--
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Re: [gmx-users] Topology for a new ligand

[Mark Abraham]

On 12/08/2011 1:48 AM, Kavyashree M wrote:

Dear users,

I was mentioning about OPLSAA force field for ATP
and other small molecule.  I just wanted to know the
procedure to be followed and some guidance from
people who have created topologies for such
molecules manually. I am going through chapter 5 of
the manual. But wanted some useful suggestions.


The link you mentioned, and links from it contain all the 
readily-available information. For ATP, you may well find a validated 
topology in the published literature.


Mark



Thank you
With Regards
M. Kavyashree


On Thu, Aug 11, 2011 at 5:03 PM, Justin A. Lemkul > wrote:




Kavyashree M wrote:

Dear gromacs users,

I wanted to know the steps to be followed
in order to generate a topology for a new
ligand. I went through the mailing list and
http://www.gromacs.org/Documentation/How-tos/Parameterization
but was not clear.


All force fields are different, and since you haven't said which
one you're trying to use there's nothing that anyone can tell you.
 Read the primary literature for the force field you want to use
and follow the procedure laid out therein.

-Justin

-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] how to calculate the conc in the genion

[Mark Abraham]

On 12/08/2011 2:22 AM, lina wrote:

On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar  wrote:

Hi,


I'd be amazed if the error was in the code and not in your calculation. The
number of water molecules doesn't matter for the calculation of the ion
concentration, of course. Pay attention to your box shape. And do consider
the number of ions has to be an integer, so for a given volume you cannot
get arbitrarily close to a given concentration.

The error is, to my humble opinion, in the reasoning. Concentration is
a macroscopic property, and when dealing with a minute volume, the
concentration of something in it is ill defined. Especially when
there's something else in that volume, taking up a significant amount
of space, like a membrane, protein or void, it becomes troublesome. I
would argue that the worst you can do in that case is take the volume
of the box and calculate the number of things to add from there to
reach a given concentration.
Whether the number of water molecules matters for the calculation of
the ion concentration depends on the unit you use for concentration.
Probably  molality is a better option than molarity. For that you do
take the number of water molecules. Frankly, that's what I usually do.
Doing so will give a desired concentration of ions in the solvent,
regardless of volume occupied by other (big) solutes or by nothing.
There is just one problem that stays nonetheless; in how far does the
bulk concentration you use as target correspond to the local
concentration you might need to use? Solutes, membranes and voids may
alter the local concentration significantly.


Yes. I do agree with you.

Here I have a field problem, I will be very glad if I can be told
which part of calculation is wrong.

a cubic box: Volumn = 101.57 *105.03 * 87.82 A  = 9.369E-25  m^3 = 93.69E-23 L
total ions: 121

so the concentration based on the box volume is:

121/AvagadroConstant/Volumn =
121/6.022E23/93.69E-23=121/6.022/9.369=0.214 mol/L?

But before when I used -conc, the number I chose maybe 0.1 or 0.15
mol/L, but not 0.2mol/L.


That's the concentration of total ions, but the concentration of each 
ionic species is about half that.


Mark



Here if consider the water, certainly the water volumn will be greatly
smaller than the box volumn, so the concentration will reach very
high?

I might be wrong in some way, hope someone can point out.

Thanks,


By the way, Lina, it would have helped if you had given the equations,
numbers and outcomes that lead you to believe there is something
wrong.

Hope it helps,

Tsjerk



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] compile template.c

[Mark Abraham]

On 12/08/2011 7:48 AM, Park, Jae Hyun nmn wrote:

Dear GMX users,

Now, I am trying to write my own gromacs analysis code with gromacs 4.5.3.
As a first test, when I run "make" in the directory of "template" I got the 
following message:

--
cc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 
-funroll-all-loops -std=gnu99 -pthread -I./include  -I/usr/include/libxml2 
-I/home/h1y/gromacs-4.5.3s/include-I/home/h1y/fftw3s/include  -c -o work.o 
work.c

cc  -L/home/h1y/gromacs-4.5.3s/lib -L/home/h1y/fftw3s/lib   -o work work.o -lmd 
-lgmx -lfftw3f -lxml2  -lnsl -lm

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x6): In function 
`vmddlopen':

: undefined reference to `dlopen'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x11): In function 
`vmddlerror':

: undefined reference to `dlerror'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x21): In function 
`vmddlsym':

: undefined reference to `dlsym'

/home/h1y/gromacs-4.5.3s/lib/libgmx.a(vmddlopen.o)(.text+0x31): In function 
`vmddlclose':

: undefined reference to `dlclose'

collect2: ld returned 1 exit status

make: *** [work] Error 1


I would deeply appreciate if any help why I got those erros and how to figure 
out.


Probably when the feature of using the VMD libraries was added, nobody 
updated share/template/Makefile.am. You can either disable the use of 
the DLOPEN facility from the VMD libraries (used for reading 
non-GROMACS-native file formats) when you configure GROMACS, or you can 
update share/template/Makefile.am so that


XLIBS = -lmd@LIBSUFFIX@ -lgmx@LIBSUFFIX@ @FFT_LIBS@ @XML_LIBS@ 
@GSL_LIBS@ @LIBS@


becomes

XLIBS = -lmd@LIBSUFFIX@ -lgmx@LIBSUFFIX@ @FFT_LIBS@ @XML_LIBS@ 
@GSL_LIBS@ @LIBS@ @DLOPEN_LIBS@


Then get the bootstrap script from a git install of GROMACS and run that 
from the main source directory, before configure, make, make install. 
Now the installed template Makefile should be able to link properly.


Mark
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[gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

[Micholas Smith]

Hi, I've checked for both libraries, they both are installed (CUDA is most definitely installed as it is used for other applications on the computer I am trying to build the mdrun-gpu binary on).-Smitty 
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Re: [gmx-users] how to calculate the conc in the genion

[lina]

On Fri, Aug 12, 2011 at 8:08 AM, Mark Abraham  wrote:
> On 12/08/2011 2:22 AM, lina wrote:
>>
>> On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar
>>  wrote:
>>>
>>> Hi,
>>>
> I'd be amazed if the error was in the code and not in your calculation.
> The
> number of water molecules doesn't matter for the calculation of the ion
> concentration, of course. Pay attention to your box shape. And do
> consider
> the number of ions has to be an integer, so for a given volume you
> cannot
> get arbitrarily close to a given concentration.
>>>
>>> The error is, to my humble opinion, in the reasoning. Concentration is
>>> a macroscopic property, and when dealing with a minute volume, the
>>> concentration of something in it is ill defined. Especially when
>>> there's something else in that volume, taking up a significant amount
>>> of space, like a membrane, protein or void, it becomes troublesome. I
>>> would argue that the worst you can do in that case is take the volume
>>> of the box and calculate the number of things to add from there to
>>> reach a given concentration.
>>> Whether the number of water molecules matters for the calculation of
>>> the ion concentration depends on the unit you use for concentration.
>>> Probably  molality is a better option than molarity. For that you do
>>> take the number of water molecules. Frankly, that's what I usually do.
>>> Doing so will give a desired concentration of ions in the solvent,
>>> regardless of volume occupied by other (big) solutes or by nothing.
>>> There is just one problem that stays nonetheless; in how far does the
>>> bulk concentration you use as target correspond to the local
>>> concentration you might need to use? Solutes, membranes and voids may
>>> alter the local concentration significantly.
>>>
>> Yes. I do agree with you.
>>
>> Here I have a field problem, I will be very glad if I can be told
>> which part of calculation is wrong.
>>
>> a cubic box: Volumn = 101.57 *105.03 * 87.82 A  = 9.369E-25  m^3 =
>> 93.69E-23 L
>> total ions: 121
>>
>> so the concentration based on the box volume is:
>>
>> 121/AvagadroConstant/Volumn =
>> 121/6.022E23/93.69E-23=121/6.022/9.369=0.214 mol/L?
>>
>> But before when I used -conc, the number I chose maybe 0.1 or 0.15
>> mol/L, but not 0.2mol/L.
>
> That's the concentration of total ions, but the concentration of each ionic
> species is about half that.

Thanks, I should not have used total number of ions.


>
> Mark
>
>>
>> Here if consider the water, certainly the water volumn will be greatly
>> smaller than the box volumn, so the concentration will reach very
>> high?
>>
>> I might be wrong in some way, hope someone can point out.
>>
>> Thanks,
>>
>>> By the way, Lina, it would have helped if you had given the equations,
>>> numbers and outcomes that lead you to believe there is something
>>> wrong.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> post-doctoral researcher
>>> Molecular Dynamics Group
>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>> * Zernike Institute for Advanced Materials
>>> University of Groningen
>>> The Netherlands
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
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>>>
>>
>>
>
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-- 
Best Regards,

lina
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