[gmx-users] error in grompp command

2014-07-02 Thread RINU KHATTRI
hello gromacs
i an working on protein ligand complex with lipid membrane (popc)

grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1

after this fatal error atomtypes CA not found
and only md.oonly mdout is formed
kindly help
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[gmx-users] Changed order of molecules in top

2014-07-02 Thread Emma Ahlstrand
Hi,

I have a problem with that the order of atoms in my topology does not match the 
order of atoms in the gro-file. I use amber99sb and I have built itp-files on 
my own for the molecules that are not present in the library. Each IMI 
contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it 
should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but 
when I run with the topology-file pasted below I get a error the this file 
contains 34 atoms.

This is my topologyfile:

; Include forcefield parameters
#include amber99sb.ff/forcefield.itp


; Additional atom types

[ atomtypes ]
; name at_name at_num mass charge   ptype  sigmaepsilon ; sw   
ref
Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ; 1
Stote Proteins 23:12 1995

; Include topology for ions
#include zn.itp

; Include water topology
#include spcetestamber.itp

; Include topology for imidazole
#include imiamberrtp.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound#mols
ZN2+ 1
IMI  2
SOL  2

-

Fatal error:
number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25)
 does not match topology (ZnHis2Wa2optM06amber.top, 34)


Since the difference is 9 atoms, I thought that the difference is one IMI, so I 
tried with one less IMI in the topology, printed below.

; Include forcefield parameters
#include amber99sb.ff/forcefield.itp


; Additional atom types

[ atomtypes ]
; name at_name at_num mass charge   ptype  sigmaepsilon ; sw   
ref
Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ; 1
Stote Proteins 23:12 1995

; Include topology for ions
#include zn.itp

; Include water topology
#include spcetestamber.itp

; Include topology for imidazole
#include imiamberrtp.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound#mols
ZN2+ 1
IMI  1
SOL  2


Then the number of atoms matches, but I get the information that the atom names 
does not match.

Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro 
does not match (C1 - ZN)
Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro 
does not match (N1 - C1)

By this message it gets clear to me that the topology makes an IMI first and 
then go on to the ZN and then probably the IMI and the two waters specified in 
the top-file. Why does it do that? And how do I correct it?

Thanks in advance for help.


--
Emma Ahlstrand
PhD student

Linnaeus University
Faculty of Health and Life Sciences
391 82 Kalmar / 351 95 Växjö

+46 480 446 152 Telephone
+46 73 905 7186 Mobile
emma.ahlstr...@lnu.se
http://lnu.se/ccbg
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[gmx-users] error in grompp command

2014-07-02 Thread ERASTOVA V.
Hi Rinu,

See what forcefield files you include in your topology, then go to the force 
field folders and check if those indeed have that atom types.
You must indeed be missing the CA type. Likely, you just forgot to include some 
topology file.

V




On 2 Jul 2014, at 10:23, 
gromacs.org_gmx-users-requ...@maillist.sys.kth.semailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se
 wrote:


--

Message: 2
Date: Wed, 2 Jul 2014 12:26:07 +0530
From: RINU KHATTRI nickname.mi...@gmail.commailto:nickname.mi...@gmail.com
To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org
Subject: [gmx-users] error in grompp command
Message-ID:
caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.commailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8

hello gromacs
i an working on protein ligand complex with lipid membrane (popc)

grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1

after this fatal error atomtypes CA not found
and only md.oonly mdout is formed
kindly help


--

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Re: [gmx-users] Some basic questions about trajconv

2014-07-02 Thread ERASTOVA V.
Hi,

trjconv is a very versatile tool.

if you do trjconv -h it will tell you:

Option -center centers the system in the box. The user can select the group
which is used to determine the geometrical center. Option -boxcenter sets the
location of the center of the box for options -pbc and -center. The center
options are: tric: half of the sum of the box vectors, rect: half of the box
diagonal, zero: zero. Use option -pbc mol in addition to -center when you
want all molecules in the box after the centering.

I think you need to use command -center in conjunction with -pbc. For -center 
select your group of atoms and for the whole trjconv you will need to select 
no-water option.

You have to play around to see what will give you necessary result. You 
possibly would need to iterate the trjconv over: 1st remove water, then centre 
atoms.

V


On 2 Jul 2014, at 10:23, 
gromacs.org_gmx-users-requ...@maillist.sys.kth.semailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se
 wrote:

--

Message: 1
Date: Wed, 2 Jul 2014 12:52:32 +0800
From: Yip Yew Mun yipy0...@gmail.commailto:yipy0...@gmail.com
To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org
Subject: [gmx-users] Some basic questions about trajconv
Message-ID: 
0e0d56b7-c31a-4170-8ef3-a879f29fd...@gmail.commailto:0e0d56b7-c31a-4170-8ef3-a879f29fd...@gmail.com
Content-Type: text/plain; charset=windows-1252

Hi all,

I?ve recently switched from AMBER and started using Gromacs. I have just ran a 
CG MD and I wish to do post-analysis on the trajectory. So if I wish to center 
my molecule in the water box, then remove the waters, what should the 
appropriate command for trajconv be?

Thanks, any help would be greatly appreciated. =)

Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry  Biological 
Chemistry
School of Physical  Mathematical Sciences | Nanyang Technological University | 
Singapore 639798
Tel: (+65) 97967803 | Email: 
yipy0...@e.ntu.edu.sgmailto:yipy0...@e.ntu.edu.sg | GMT+8h

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[gmx-users] restart the calculation----- checksum error

2014-07-02 Thread Guo, Yanan (IPC)
Hello dear gmx-users,

I tried to restart the calculation, but there is always one checksum error as:

Program mdrun_mpi, VERSION 4.6.1
Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c, 
line: 2155

Fatal error:
Checksum wrong for 'pull.xvg'. The file has been replaced or its contents have 
been modified. Cannot do appending because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


But I did nothing to this pull.xvg file..

I ever did this restarting before, and I found if I didn't output the  (xx).xvg 
file, the restarting calculation works.

So one solution maybe that I redo the calcuation without outputting the 
pull.xvg filebut it will takes quite a long time again...

Anybody has some suggestions? 

Thank you so much!

Best 
Yanan
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Re: [gmx-users] obtaining .gro timeframe

2014-07-02 Thread Justin Lemkul



On 7/1/14, 11:28 PM, Chetan Mahajan wrote:

Thanks, Justin. *Until now, I was thinking that xtc coordinates are
wrapped. It's good to know that coordinates from xtc files are unwrapped
(please comment if not correct, since we talked only with respect to gro


That is correct.  mdrun doesn't care about our visualization convenience.  No 
sense in wasting performance doing imaging on the fly when it's not necessary.



file). *But I am confused at another thing. I have known at the origin of
the box is at one of its vertices ( is that not true?). *Then why are some
coordinates in .gro file (the one generated at the end of gromacs MD run)
negative, if coordinates are wrapped in the box?*



Molecules are made whole; sometimes they're translated in the positive 
direction, sometimes in the negative direction, depending on how the molecule is 
being reconstructed.



Is my original command using trjconv okay?



OK is relative.  In this case, you seem troubled by the slight difference in 
convention, but there's nothing wrong with the command.  If you want trjconv 
to make molecules whole, use -pbc mol or -pbc whole.  Your original command 
simply dumps the coordinates and does nothing about periodicity.



Whereas I do get a sample x-coordinate in .gro file, generated at the end
of MD run (let's call it gro1) from that in .gro file, generated using
trjconv on xtc (let's call it gro2) by adding a box length to concerned
coordinate in gro2, (as shown in excerpt 1) , it's only by subtracting a
boxlength that we interconvert between similar values, as shown in excerpt
2 of the SAME file. *Why is there no consistency of conversion between SAME
two .gro files for all the coordinates? How do I mathematically obtain file
2 from file 1 with some consistent measure?  *



See above.  trjconv will do it for you.

-Justin


- : for .gro file at the end of gromacs MD run (gro1)
+ : for .gro timeframe file obtained from .xtc trajectory ( using trjconv)
(gro2)

*EXCERT 1*

-   11SOLHW1 2188   3.244   3.071  10.934
-   11SOLHW2 2189   3.211   2.940  10.842
+   11SOLHW1 2188   0.023   3.071  10.934
+   11SOLHW2 2189  -0.011   2.940  10.842


*EXCERT 2*
-   56SOLHW1 2323  -0.031   1.076   1.130
-   56SOLHW2 2324  -0.040   1.096   1.292
+   56SOLHW1 2323   3.191   1.076   1.130
+   56SOLHW2 2324   3.182   1.096   1.292

Thanks
Chetan

On Tue, Jul 1, 2014 at 8:10 PM, Justin Lemkul jalem...@vt.edu wrote:




On 7/1/14, 9:08 PM, Chetan Mahajan wrote:


Thanks, Justin. Are you saying, the coordinates in .gro  file extracted
from xtc trajectory are not wrapped, whereas those in the .gro file
generated at the end of gromacs MD run are wrapped in the box?



Yes, unless you've manipulated the trajectory in some way with trjconv
beforehand.


  Now I have a question:  the negative coordinates that are present in the

following text are from .gro file (generated at the end of MD run),
whereas
positive ones are from .gro file obtained using trjconv on xtc.



Either way, it's a periodicity effect.  Molecules are made whole.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Inserting required no. of water using genbox -ci -nmol crashing

2014-07-02 Thread Justin Lemkul



On 7/2/14, 12:02 AM, shivangi nangia wrote:

Hello gmx-users,

This is regarding inserting required number of TIP3P water molecules using
genbox.

I have a system containing POPC, peptide, water molecules  ions.

For some system set up, I had to delete all the waters and ions ( The box
size was not changed). Now I  want to insert the same number of water
molecules back into the box (35228) but the job keeps crashing. When I run
it interactively it says there is not enough memory and if I submit in
queue the job just exits or goes into zombie mode.

System size: 9.38943   9.38943  15.54950

command: genbox_mpi -cp  popc_pep.gro -ci spc.gro -nmol 35228 -o
solvated.gro

I have tried varied kinds of spc.gro containing just one water molecule, 2
,3 and 4 (system size fixed accordingly using editconf -d 0 )

On using -cs option, lesser number of water molecules get inserted than
35228 on using the spc216.gro found in the /apps/gromacs/top folder.



That means there's not enough room in the box for that many waters in those 
given configurations.  You run out of memory because (1) using -ci -nmol is a 
horribly inefficient way to insert waters and (2) genbox simply can't find 
enough space, so it keeps going until system resources are exhausted.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] TOP file conversion

2014-07-02 Thread Justin Lemkul



On 7/2/14, 12:27 AM, Andy Chao wrote:

Dear GROMACS Users:

I would like to convert a GRO file to the TOP file.  Is it a better way to
use
pdb2gmx -f device.gro -p device.top

or to use

g_x2top -f device.gro -ff oplsaa -o device.top?



That depends.  If the contents of device.gro consist of a linear polymer of 
definable units in the .rtp file, pdb2gmx is the way to go.  If it is non-linear 
or you don't have suitable .rtp entries, g_x2top may be better.  In theory, you 
can accomplish an equivalent result with either, but without more detail of 
what's going on, there's no real solid recommendation to make.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] error in grompp command

2014-07-02 Thread Justin Lemkul



On 7/2/14, 6:07 AM, RINU KHATTRI wrote:

hello gromacs users
  i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the
place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are
present according to tutorial i have been followed  all the step
still em.tpr not formed
atomtype CA not found



CA is the gmx.ff nomenclature for the calcium type, so that suggests you're 
mixing and matching force fields (note that gmx.ff has been removed from the 
latest Gromacs version, since it should not be used).  Without explicit detail 
of your topology (i.e. post your files so they can be downloaded), there's very 
little that can be done to suggest where things have gone wrong.  I strongly 
suspect you've mixed and matched force fields somewhere, which is easy to do 
when dealing with complex systems.  Pick a force field, stick to it exactly.


-Justin



On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. valentina.erast...@durham.ac.uk

wrote:



Hi Rinu,

See what forcefield files you include in your topology, then go to the
force field folders and check if those indeed have that atom types.
You must indeed be missing the CA type. Likely, you just forgot to include
some topology file.

V




On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-requ...@maillist.sys.kth.se
mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:


--

Message: 2
Date: Wed, 2 Jul 2014 12:26:07 +0530
From: RINU KHATTRI nickname.mi...@gmail.commailto:
nickname.mi...@gmail.com
To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org
Subject: [gmx-users] error in grompp command
Message-ID:
caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com
mailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com



Content-Type: text/plain; charset=UTF-8

hello gromacs
i an working on protein ligand complex with lipid membrane (popc)

grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1

after this fatal error atomtypes CA not found
and only md.oonly mdout is formed
kindly help


--

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--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] restart the calculation----- checksum error

2014-07-02 Thread Justin Lemkul



On 7/2/14, 5:59 AM, Guo, Yanan (IPC) wrote:

Hello dear gmx-users,

I tried to restart the calculation, but there is always one checksum error as:

Program mdrun_mpi, VERSION 4.6.1
Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c, 
line: 2155

Fatal error:
Checksum wrong for 'pull.xvg'. The file has been replaced or its contents have 
been modified. Cannot do appending because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


But I did nothing to this pull.xvg file..

I ever did this restarting before, and I found if I didn't output the  (xx).xvg 
file, the restarting calculation works.

So one solution maybe that I redo the calcuation without outputting the 
pull.xvg filebut it will takes quite a long time again...

Anybody has some suggestions?



Tell mdrun not to append, and just concatenate the files later.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Changed order of molecules in top

2014-07-02 Thread Justin Lemkul



On 7/2/14, 3:31 AM, Emma Ahlstrand wrote:

Hi,

I have a problem with that the order of atoms in my topology does not match the order of 
atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the 
molecules that are not present in the library. Each IMI contains 9 atoms and 
each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in 
total, which is present in the .gro file, but when I run with the topology-file pasted 
below I get a error the this file contains 34 atoms.

This is my topologyfile:

; Include forcefield parameters
#include amber99sb.ff/forcefield.itp


; Additional atom types

[ atomtypes ]
; name at_name at_num mass charge   ptype  sigmaepsilon ; sw   
ref
Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ; 1
Stote Proteins 23:12 1995

; Include topology for ions
#include zn.itp

; Include water topology
#include spcetestamber.itp

; Include topology for imidazole
#include imiamberrtp.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound#mols
ZN2+ 1
IMI  2
SOL  2

-

Fatal error:
number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25)
  does not match topology (ZnHis2Wa2optM06amber.top, 34)


Since the difference is 9 atoms, I thought that the difference is one IMI, so I 
tried with one less IMI in the topology, printed below.

; Include forcefield parameters
#include amber99sb.ff/forcefield.itp


; Additional atom types

[ atomtypes ]
; name at_name at_num mass charge   ptype  sigmaepsilon ; sw   
ref
Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ; 1
Stote Proteins 23:12 1995

; Include topology for ions
#include zn.itp

; Include water topology
#include spcetestamber.itp

; Include topology for imidazole
#include imiamberrtp.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
11   1000   1000   1000
#endif

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound#mols
ZN2+ 1
IMI  1
SOL  2


Then the number of atoms matches, but I get the information that the atom names 
does not match.

Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro 
does not match (C1 - ZN)
Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro 
does not match (N1 - C1)

By this message it gets clear to me that the topology makes an IMI first and 
then go on to the ZN and then probably the IMI and the two waters specified in 
the top-file. Why does it do that? And how do I correct it?



No, your coordinate file has IMI first.  grompp expects the input coordinates 
and topology to be in the same order.  You list Zn, IMI, and SOL in the .top - 
that is the expected order in the coordinates.  As reported by grompp, that is 
not the case.  There should be no probably here; with such a small system it 
should be very easy to inspect the .gro file in a text editor and see precisely 
what is going on.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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[gmx-users] Use trjconv in parallel,

2014-07-02 Thread ABEL Stephane 175950
Hello, 

in short : it is possible ? I use the gromacs v4.6.5. 

Thanks 

Stéphane
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Re: [gmx-users] Use trjconv in parallel,

2014-07-02 Thread Carsten Kutzner

On 02 Jul 2014, at 12:55, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello, 
 
 in short : it is possible ? I use the gromacs v4.6.5. 
No.

Carsten
 
 Thanks 
 
 Stéphane
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Re: [gmx-users] grompp does not find atomtype

2014-07-02 Thread Justin Lemkul



On 7/2/14, 4:40 AM, Dawid das wrote:

I have managed to deal with this problem in following way:

In topology file some bonding parameters were actually missing but some
bonding parameters were not needed, e.g. U-B or dihedral parameters for
atoms which are not connected, that is they belong to different parts of my
new residue.
I found parameters for the missing ones and hashed (;) them out. Is it what
I can do? Like I say, theses bonding parameters that I hashed out were for
atom types which are not connected directly.

Then I performed minimization with steepest descent and in output file I
got:

  4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep=  426, Dmax= 2.5e-06 nm,
Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep=  427, Dmax= 1.2e-06
nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax  1000

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 428 steps,
but did not reach the requested Fmax  1000.
Potential Energy  = -4.5465475e+05
Maximum force =  1.7057922e+04 on atom 1003
Norm of force =  1.1677969e+02

But I continued with NVT MD simulation. This is my nvt-md.mdp file:

title   = NVT MD
integrator  = md
constraints = all-bonds
dt  = 0.001
nsteps  = 2
nstenergy   = 100
nstlist = 10
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog  = 100
nstxtcout   = 1000
xtcprecision= 500
ns_type = grid
coulombtype = PME
rlist   = 1.0
rcoulomb= 1.0
rvdw= 1.0


These cutoffs are incorrect for using CHARMM force fields.  See previous posts 
on proper settings.



tcoupl  = nose-hoover
tc-grps = Protein SOL NA
tau_t   = 0.1 0.1 0.1 ;(3 numbers - because 3 tc-grps)
ref_t   = 100 100 100 ;(3 numbers - because 3 tc-grps)


Coupling water and ions separately is not sensible.

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do


Pcoupl  = No
gen_vel = yes
gen_temp= 100
gen_seed= 173529
energygrps  = Protein  SOL NA
constraint_algorithm = LINCS
pbc = xyz

And in my NVT output I got error for LINCS:

relative constraint deviation after LINCS:
rms 0.036755, max 1.509884 (between atoms 998 and 1000)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
1001   1003   62.10.1410   0.2032  0.1410
1001   1002   68.10.1240   0.1962  0.1240
1000   1001   88.10.1460   0.3276  0.1460
 998   1000   90.00.1390   0.3489  0.1390
 986   1000   90.70.1400   0.2237  0.1400
 985986   30.70.1300   0.1499  0.1300
Wrote pdb files with previous and current coordinates


These atoms are those for my new residue. For next step I get more
constraint deviation.
Now, is it possible that this is because of wrong parameters? Or maybe I
should minimize my system further?
Here are all the files:

http://www.speedyshare.com/jjvgd/md-simul.tar.bz2



When sharing files, please only post what is actually necessary to reproduce the 
problem - a self-contained force field directory, coordinates, topology, .mdp, 
and index file if needed.  A dump of dozens of files with no context gets 
burdensome to go through.


Your minimized geometry is clearly junk.  Just visualize the structure and you 
will see that your mCherry residue is completely distorted.  The very large 
(10^4) force after EM should have been the first clue that something is very wrong.


The problems almost certainly stem from the manipulations you've made to the 
angles and dihedrals.  I don't understand why you've commented some of them out. 
 For instance, the first angle that you've removed is atoms 977-978-992, which 
clearly should have an angle interaction because 977-978 and 978-992 are bonded. 
 Simply removing inconvenient interactions (i.e. lacking parameters or 
whatever) leads to a total meltdown of the model.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] grompp erros

2014-07-02 Thread Justin Lemkul



On 7/2/14, 5:39 AM, Linlin Sun wrote:

Hello everyone,

In order to build a virtual site which is independent from other structure,
I have created a new atom type and set the mass of this new atom type to
zero. However, when I use* grompp*, it failed with fatal errors, which
complain about the zero mass of the new atom type.

Anyone could possibly know how to get around this problem? Any suggestions
would be helpful. Thanks very much!



If you've declared it as an atom (particle type A), then that's probably why 
you're getting this error.  Virtual site types are particle type V in 
ffnonbonded.itp.  I guess the larger point is - why have a virtual site that is 
not dependent upon any other elements of the structure?


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Use trjconv in parallel

2014-07-02 Thread ABEL Stephane 175950
Thanks for your quick and also fast (;)) reply, Carsten. 

Stéphane


--

Message: 4
Date: Wed, 2 Jul 2014 10:55:45 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
To: gromacs.org_gmx-users@maillist.sys.kth.se
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Use trjconv in parallel,
Message-ID:
3e39b768bb199548ab18f7289e7534af1b24f...@exdag0-b0.intra.cea.fr
Content-Type: text/plain; charset=iso-8859-1

Hello,

in short : it is possible ? I use the gromacs v4.6.5.

Thanks

St?phane

--

Message: 5
Date: Wed, 2 Jul 2014 13:44:08 +0200
From: Carsten Kutzner ckut...@gwdg.de
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Use trjconv in parallel,
Message-ID: 39b862ce-6e52-4590-9c57-ba34864b2...@gwdg.de
Content-Type: text/plain; charset=iso-8859-1


On 02 Jul 2014, at 12:55, ABEL Stephane 175950 stephane.a...@cea.fr wrote:

 Hello,

 in short : it is possible ? I use the gromacs v4.6.5.
No.

Carsten

 Thanks

 St?phane
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Message: 6
Date: Wed, 02 Jul 2014 07:50:34 -0400
From: Justin Lemkul jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] grompp does not find atomtype
Message-ID: 53b3f20a.7060...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



On 7/2/14, 4:40 AM, Dawid das wrote:
 I have managed to deal with this problem in following way:

 In topology file some bonding parameters were actually missing but some
 bonding parameters were not needed, e.g. U-B or dihedral parameters for
 atoms which are not connected, that is they belong to different parts of my
 new residue.
 I found parameters for the missing ones and hashed (;) them out. Is it what
 I can do? Like I say, theses bonding parameters that I hashed out were for
 atom types which are not connected directly.

 Then I performed minimization with steepest descent and in output file I
 got:

   4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep=  426, Dmax= 2.5e-06 nm,
 Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep=  427, Dmax= 1.2e-06
 nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M
 Stepsize too small, or no change in energy.
 Converged to machine precision,
 but not to the requested precision Fmax  1000

 Double precision normally gives you higher accuracy.
 You might need to increase your constraint accuracy, or turn
 off constraints alltogether (set constraints = none in mdp file)

 writing lowest energy coordinates.

 Steepest Descents converged to machine precision in 428 steps,
 but did not reach the requested Fmax  1000.
 Potential Energy  = -4.5465475e+05
 Maximum force =  1.7057922e+04 on atom 1003
 Norm of force =  1.1677969e+02

 But I continued with NVT MD simulation. This is my nvt-md.mdp file:

 title   = NVT MD
 integrator  = md
 constraints = all-bonds
 dt  = 0.001
 nsteps  = 2
 nstenergy   = 100
 nstlist = 10
 nstxout = 1000
 nstvout = 1000
 nstfout = 0
 nstlog  = 100
 nstxtcout   = 1000
 xtcprecision= 500
 ns_type = grid
 coulombtype = PME
 rlist   = 1.0
 rcoulomb= 1.0
 rvdw= 1.0

These cutoffs are incorrect for using CHARMM force fields.  See previous posts
on proper settings.

 tcoupl  = nose-hoover
 tc-grps = Protein SOL NA
 tau_t   = 0.1 0.1 0.1 ;(3 numbers - because 3 tc-grps)
 ref_t   = 100 100 100 ;(3 numbers - because 3 tc-grps)

Coupling water and ions separately is not sensible.

http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do

 Pcoupl  = No
 gen_vel = yes
 gen_temp= 100
 gen_seed= 173529
 energygrps  = Protein  SOL NA
 constraint_algorithm = LINCS
 pbc = xyz

 And in my NVT output I got error for LINCS:

 relative constraint deviation after LINCS:
 rms 0.036755, max 1.509884 (between atoms 998 and 1000)
 bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
 1001   1003   62.10.1410   0.2032  0.1410
 1001   1002   68.10.1240   0.1962  0.1240
 1000   1001   88.10.1460   0.3276  0.1460
  998   1000   90.00.1390   0.3489  0.1390
  986   1000   90.70.1400   0.2237  0.1400
  985986   30.70.1300   0.1499  0.1300
 Wrote pdb files with previous and current coordinates


 These atoms are those for my new residue. For next step 

[gmx-users] Problem with g_chi options

2014-07-02 Thread Anna Stopka

Hi,

I want do an analysis of my simulation with the tool g_chi.
The problem is, that the optional output options don't work.

I use the following command:

g_chi -s config.gro -f traj.xtc -oh -all

and all I get are the standard output files chi.log and order.xvg.
I am not sure if it has something to do with the following warning I get:

WARNING: not all dihedrals found in topology (only 1056 out of 1746)!

Honestly, I don't understand why I get this warning, because all the 
input files are fine.


Thanks for your help!
Best regards,
Anna
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Re: [gmx-users] grompp does not find atomtype

2014-07-02 Thread Justin Lemkul



On 7/2/14, 9:22 AM, Dawid das wrote:

2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu:


The problems almost certainly stem from the manipulations you've made to
the angles and dihedrals.  I don't understand why you've commented some of
them out.  For instance, the first angle that you've removed is atoms
977-978-992, which clearly should have an angle interaction because 977-978
and 978-992 are bonded.  Simply removing inconvenient interactions (i.e.
lacking parameters or whatever) leads to a total meltdown of the model.





Okey, but what should I do if there are missing parameters for combination
of atoms which are not bonded?
For instance: 973-977-978-992 atoms are not bonded but still in *top there
is an torsion interaction for these atoms? What does it mean? It seems
like some of the atom types are confused? Is it possible that I defined
them in ambigous way?



Introduction of custom atom types requires introduction of associated bonded 
parameters.  You can't introduce atoms without defining all the ways that they 
interact.  The proper approach is to add suitable parameters in ffbonded.itp or 
in the .top itself.  If you don't have those parameters, you need to derive them 
or obtain them from some reliable source.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] grompp does not find atomtype

2014-07-02 Thread Dawid das
Beside that, why do you say that 978-992 are bonded? According to visual
inspection of mCherry7-solv-ion.gro there is no connection between them (as
it should be) and also in mCherry7.top there is no bonding parameter for
them.


2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com:


 2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu:

 The problems almost certainly stem from the manipulations you've made to
 the angles and dihedrals.  I don't understand why you've commented some of
 them out.  For instance, the first angle that you've removed is atoms
 977-978-992, which clearly should have an angle interaction because 977-978
 and 978-992 are bonded.  Simply removing inconvenient interactions (i.e.
 lacking parameters or whatever) leads to a total meltdown of the model.




 Okey, but what should I do if there are missing parameters for combination
 of atoms which are not bonded?
 For instance: 973-977-978-992 atoms are not bonded but still in *top there
 is an torsion interaction for these atoms? What does it mean? It seems
 like some of the atom types are confused? Is it possible that I defined
 them in ambigous way?

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Re: [gmx-users] grompp does not find atomtype

2014-07-02 Thread Dawid das
Excuse me but I don't think we understand each other. If there are three
atoms for instance and two of them are bonded and the third is not then how
can I obtain or derive parameters for them? That is what I do not
understand.



2014-07-02 15:29 GMT+02:00 Dawid das add...@googlemail.com:

 Beside that, why do you say that 978-992 are bonded? According to visual
 inspection of mCherry7-solv-ion.gro there is no connection between them (as
 it should be) and also in mCherry7.top there is no bonding parameter for
 them.


 2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com:


 2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu:

 The problems almost certainly stem from the manipulations you've made to
 the angles and dihedrals.  I don't understand why you've commented some of
 them out.  For instance, the first angle that you've removed is atoms
 977-978-992, which clearly should have an angle interaction because 977-978
 and 978-992 are bonded.  Simply removing inconvenient interactions (i.e.
 lacking parameters or whatever) leads to a total meltdown of the model.




 Okey, but what should I do if there are missing parameters for
 combination of atoms which are not bonded?
 For instance: 973-977-978-992 atoms are not bonded but still in *top
 there is an torsion interaction for these atoms? What does it mean? It
 seems like some of the atom types are confused? Is it possible that I
 defined them in ambigous way?



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Re: [gmx-users] grompp does not find atomtype

2014-07-02 Thread Justin Lemkul



On 7/2/14, 9:29 AM, Dawid das wrote:

Beside that, why do you say that 978-992 are bonded? According to visual
inspection of mCherry7-solv-ion.gro there is no connection between them (as
it should be) and also in mCherry7.top there is no bonding parameter for
them.



Inspection of a coordinate file tells you nothing about the bonded structure. 
Look at the topology, line 4712:


   978   992 10.1350 127612.0

That says atoms 978 and 992 are bonded, and you have defined the parameters for 
that bond manually.


-Justin



2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com:



2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu:

The problems almost certainly stem from the manipulations you've made to

the angles and dihedrals.  I don't understand why you've commented some of
them out.  For instance, the first angle that you've removed is atoms
977-978-992, which clearly should have an angle interaction because 977-978
and 978-992 are bonded.  Simply removing inconvenient interactions (i.e.
lacking parameters or whatever) leads to a total meltdown of the model.





Okey, but what should I do if there are missing parameters for combination
of atoms which are not bonded?
For instance: 973-977-978-992 atoms are not bonded but still in *top there
is an torsion interaction for these atoms? What does it mean? It seems
like some of the atom types are confused? Is it possible that I defined
them in ambigous way?



--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Changed order of molecules in top

2014-07-02 Thread Emma A
Justin Lemkul jalemkul@... writes:

 
 
 On 7/2/14, 3:31 AM, Emma Ahlstrand wrote:
  Hi,
 
  I have a problem with that the order of atoms in my topology does not
match the order of atoms in the gro-file.
 I use amber99sb and I have built itp-files on my own for the molecules
that are not present in the library.
 Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so
in total it should be 9*2+3*2+1=25
 atoms in total, which is present in the .gro file, but when I run with the
topology-file pasted below I get a
 error the this file contains 34 atoms.
 
  This is my topologyfile:
 
  ; Include forcefield parameters
  #include amber99sb.ff/forcefield.itp
 
 
  ; Additional atom types
 
  [ atomtypes ]
  ; name at_name at_num mass charge   ptype  sigmaepsilon
; sw   ref
  Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ;
1Stote Proteins 23:12 1995
 
  ; Include topology for ions
  #include zn.itp
 
  ; Include water topology
  #include spcetestamber.itp
 
  ; Include topology for imidazole
  #include imiamberrtp.itp
 
  #ifdef POSRES_WATER
  ; Position restraint for each water oxygen
  [ position_restraints ]
  ;  i funct   fcxfcyfcz
  11   1000   1000   1000
  #endif
 
  [system ]
  ; Name
  ZnHis2Wa2
 
  [ molecules ]
  ; Compound#mols
  ZN2+ 1
  IMI  2
  SOL  2
 
  -
 
  Fatal error:
  number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25)
does not match topology (ZnHis2Wa2optM06amber.top, 34)
 
 
  Since the difference is 9 atoms, I thought that the difference is one
IMI, so I tried with one less IMI in the
 topology, printed below.
 
  ; Include forcefield parameters
  #include amber99sb.ff/forcefield.itp
 
 
  ; Additional atom types
 
  [ atomtypes ]
  ; name at_name at_num mass charge   ptype  sigmaepsilon
; sw   ref
  Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ;
1Stote Proteins 23:12 1995
 
  ; Include topology for ions
  #include zn.itp
 
  ; Include water topology
  #include spcetestamber.itp
 
  ; Include topology for imidazole
  #include imiamberrtp.itp
 
  #ifdef POSRES_WATER
  ; Position restraint for each water oxygen
  [ position_restraints ]
  ;  i funct   fcxfcyfcz
  11   1000   1000   1000
  #endif
 
  [system ]
  ; Name
  ZnHis2Wa2
 
  [ molecules ]
  ; Compound#mols
  ZN2+ 1
  IMI  1
  SOL  2
 
 
  Then the number of atoms matches, but I get the information that the
atom names does not match.
 
  Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and
ZnHis2Wa2optM06.gro does not match (C1 - ZN)
  Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and
ZnHis2Wa2optM06.gro does not match (N1 - C1)
 
  By this message it gets clear to me that the topology makes an IMI first
and then go on to the ZN and then
 probably the IMI and the two waters specified in the top-file. Why does it
do that? And how do I correct it?
 
 
 No, your coordinate file has IMI first.  grompp expects the input coordinates 
 and topology to be in the same order.  You list Zn, IMI, and SOL in the
.top - 
 that is the expected order in the coordinates.  As reported by grompp,
that is 
 not the case.  There should be no probably here; with such a small
system it 
 should be very easy to inspect the .gro file in a text editor and see
precisely 
 what is going on.
 
 -Justin
 
Hi Justin,
the problem is that my coordinate file (ZnHis2Wa2optM06.gro) has Zn first
and then two IMI and then two water and this is what I think I make with my
topology file as well, but the topology seems to produce an IMI first? 

ZnHis2Wa2
   25
1Zn++ZN1   1.495   1.497   1.361
2MOL C12   1.293   1.499   1.588
2MOL N13   1.324   1.561   1.451
2MOL C24   1.166   1.556   1.632
...
Regards,
Emma

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Re: [gmx-users] Changed order of molecules in top

2014-07-02 Thread Justin Lemkul



On 7/2/14, 9:48 AM, Emma A wrote:

Justin Lemkul jalemkul@... writes:




On 7/2/14, 3:31 AM, Emma Ahlstrand wrote:

Hi,

I have a problem with that the order of atoms in my topology does not

match the order of atoms in the gro-file.

I use amber99sb and I have built itp-files on my own for the molecules

that are not present in the library.

Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so

in total it should be 9*2+3*2+1=25

atoms in total, which is present in the .gro file, but when I run with the

topology-file pasted below I get a

error the this file contains 34 atoms.


This is my topologyfile:

; Include forcefield parameters
#include amber99sb.ff/forcefield.itp


; Additional atom types

[ atomtypes ]
; name at_name at_num mass charge   ptype  sigmaepsilon

; sw   ref

Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ;

1Stote Proteins 23:12 1995


; Include topology for ions
#include zn.itp

; Include water topology
#include spcetestamber.itp

; Include topology for imidazole
#include imiamberrtp.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
 11   1000   1000   1000
#endif

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound#mols
ZN2+ 1
IMI  2
SOL  2

-

Fatal error:
number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25)
   does not match topology (ZnHis2Wa2optM06amber.top, 34)


Since the difference is 9 atoms, I thought that the difference is one

IMI, so I tried with one less IMI in the

topology, printed below.


; Include forcefield parameters
#include amber99sb.ff/forcefield.itp


; Additional atom types

[ atomtypes ]
; name at_name at_num mass charge   ptype  sigmaepsilon

; sw   ref

Zn++  Zn++30 65.37000  2.000A1.94216e-01  1.046   ;

1Stote Proteins 23:12 1995


; Include topology for ions
#include zn.itp

; Include water topology
#include spcetestamber.itp

; Include topology for imidazole
#include imiamberrtp.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
 11   1000   1000   1000
#endif

[system ]
; Name
ZnHis2Wa2

[ molecules ]
; Compound#mols
ZN2+ 1
IMI  1
SOL  2


Then the number of atoms matches, but I get the information that the

atom names does not match.


Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and

ZnHis2Wa2optM06.gro does not match (C1 - ZN)

Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and

ZnHis2Wa2optM06.gro does not match (N1 - C1)


By this message it gets clear to me that the topology makes an IMI first

and then go on to the ZN and then

probably the IMI and the two waters specified in the top-file. Why does it

do that? And how do I correct it?




No, your coordinate file has IMI first.  grompp expects the input coordinates
and topology to be in the same order.  You list Zn, IMI, and SOL in the

.top -

that is the expected order in the coordinates.  As reported by grompp,

that is

not the case.  There should be no probably here; with such a small

system it

should be very easy to inspect the .gro file in a text editor and see

precisely

what is going on.

-Justin


Hi Justin,
the problem is that my coordinate file (ZnHis2Wa2optM06.gro) has Zn first
and then two IMI and then two water and this is what I think I make with my
topology file as well, but the topology seems to produce an IMI first?

ZnHis2Wa2
25
 1Zn++ZN1   1.495   1.497   1.361
 2MOL C12   1.293   1.499   1.588
 2MOL N13   1.324   1.561   1.451
 2MOL C24   1.166   1.556   1.632
 ...


Without seeing the full contents of all the files, none of this really makes 
sense.  If you can provide a link to download the full (1) topology and all 
related .itp files, (2) coordinates, and (3) .mdp files, I will take a look.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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[gmx-users] Graphene topology file

2014-07-02 Thread #SUKRITI GUPTA#
Dear all,


I want to simulate graphite in water, for which i am trying to create a 
topology file for graphite. As its .rtp file cannot be written correctly, i 
tried to use g_x2top command following the steps given in following tutorial.

http://chembytes.wikidot.com/grocnt


But I think this tutorial is quite old and hence suitable for older version of 
gromacs as it still uses FF.dat file. Moreover if i am trying to make a new 
forcefield directory with name graphite_oplsaa containing the modified files 
like .n2t,.rtp and .itp, its giving me an error that Could not find force 
field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. 
When I try to add this forcefield in original path ie. user/share/gromacs/top, 
it does not allow me to do that as i am not the administrator. Can anyone 
please let me know how to create the topology file. I require 3 graphene sheets 
with pbc. I have created the .pdb file using nanobuilder in vmd.


Thanks and Regards

Sukriti


[https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcQuwIkOr74lrv1_LpOuPBiUQ7Ai2kV8dmaAKtXKB0KYMUKxiIHSJg]
 
http://www.google.com/imgres?imgurl=http%3A%2F%2Fwww.spms.ntu.edu.sg%2Fmas%2Fconference%2Ficits2013%2FICITS-2013-files%2Fntu-logo.jpgimgrefurl=http%3A%2F%2Fwww.spms.ntu.edu.sg%2Fmas%2Fconference%2Ficits2013%2Fh=59w=150tbnid=dMsKki52xFWVeM%3Azoom=1docid=XqAK8OLvcu_FUMei=xVyyU5q9A87j8AWMzYG4Cwtbm=ischved=0CFgQMygxMDEiact=rcuact=3dur=1673page=3start=41ndsp=27
Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
http://maps.ntu.edu.sg/maps#q:research%20techno%20plaza%20%28rtp%29
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, 
Singapore(637459)
Tel: (65) 81164191 GMT+8h | 
Email:sukriti...@e.ntu.edu.sgmailto:xx...@e.ntu.edu.sg | Web:erian.ntu.edu.sg 
http://www.ntu.edu.sg/home/xuzc/People.html
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Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-02 Thread Nikolaos Michelarakis
Dear Justin,

Thank you very much for your reply. I have tried the converter but I think
I don't have enough experience to get the CHARMM files working properly
with the converter. If I sent you the files, would it be possible to do it
for me or guide me through it?

Thanks again,

Nicholas


On 23 June 2014 17:42, Justin Lemkul jalem...@vt.edu wrote:



 On 6/23/14, 9:48 AM, Nikolaos Michelarakis wrote:

 Dear All,

 First, I would like to say that I have started using GROMACS during this
 last month so please take that in mind when answering.

 I am trying to run an MD simulation of an enzyme which contains some non
 standard residues such as a tungsten metal ion and some other cofactors. I
 understand that I need to create the topology and find the parameters for
 these non-standard residues. Reading the manual I saw about .itp files
 and,
 correct me if I'm wrong, but it's my understanding that these are used for
 parts of the topology which are not bonded or intergrated in the structure
 that is being simulated. My question is how do I include these bonded
 parts
 in the simulation?


 An .itp file specifies a distinct [moleculetype] that shares no bonded
 interactions with any other species in the system.  The development version
 of the code has the capability to do intermolecular bondeds, but at present
 the distinction is true enough.  Are you asking how to include actual bonds
 between your non-standard residues and other parts of the system?  If so,
 then the only options are:

 1. Create an .rtp entry for your non-standard residue(s) and modify
 specbond.dat accordingly, as these will likely be non-linear bonds.  That
 way, you'll have a single [moleculetype] in which you will have bonds
 between the different residues.

 2. Use git to obtain the developmental version of the code that has
 intermolecular bond capabilities.  I don't recall offhand which patch has
 it or if it's even been merged, but it's in the Gerrit repo, at least.


  My second question, someone has already developed a topology and some
 parameters for this structure but in CHARM. I tried using one of the two
 scripts available online to convert them to GROMACS but to no avail. Is
 there a way to automatically do this or will I have to go all over it by
 hand?


 If you have a stream file, we have a converter:

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

 It was designed to interface with CGenFF .str files from ParamChem, but it
 should do the job.

 -Justin

 --
 ==

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

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

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

 ==
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Re: [gmx-users] Changed order of molecules in top

2014-07-02 Thread Emma A
 Without seeing the full contents of all the files, none of this really makes 
 sense.  If you can provide a link to download the full (1) topology and all 
 related .itp files, (2) coordinates, and (3) .mdp files, I will take a look.
 
 -Justin
 

Hi again,
thanks a lot for taking your time.
Here is a link to the top (and test.top with just one IMI), the gro, the
itp´s, and the mdp files.
https://www.dropbox.com/s/dmz41drsjr0bqkn/ZnHis2Wa2.tar.gz
I hope this kind of link works.
Best regards,
Emma


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Re: [gmx-users] Changed order of molecules in top

2014-07-02 Thread Justin Lemkul


On 7/2/14, 11:17 AM, Emma A wrote:

Without seeing the full contents of all the files, none of this really makes
sense.  If you can provide a link to download the full (1) topology and all
related .itp files, (2) coordinates, and (3) .mdp files, I will take a look.

-Justin



Hi again,
thanks a lot for taking your time.
Here is a link to the top (and test.top with just one IMI), the gro, the
itp´s, and the mdp files.
https://www.dropbox.com/s/dmz41drsjr0bqkn/ZnHis2Wa2.tar.gz
I hope this kind of link works.
Best regards,
Emma




Here's your problem:

[ molecules ]
; Compound#mols
IMI 1

is in imiamberrtp.itp and it should not be.  An .itp file specifies a 
[moleculetype] and associated parameters.  The [system] and [molecules] 
directives are system-level instructions.  So what's happening is you're telling 
grompp that there is an IMI molecule as soon as you #include the .itp file.  A 
bit surprising that there aren't any other fatal errors, because technically 
this breaks the topology order.  Remove [system] and [molecules] from this .itp 
file, correct the [molecules] directive to specify 2 IMI in the .top, and you 
should be fine.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Graphene topology file

2014-07-02 Thread Justin Lemkul



On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:

Dear all,


I want to simulate graphite in water, for which i am trying to create a 
topology file for graphite. As its .rtp file cannot be written correctly, i 
tried to use g_x2top command following the steps given in following tutorial.

http://chembytes.wikidot.com/grocnt


But I think this tutorial is quite old and hence suitable for older version of gromacs as 
it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory 
with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its 
giving me an error that Could not find force field 'graphite_oplsaa' in current 
directory, install tree or GMXDATA path. When I try to add this forcefield in 
original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the 
administrator. Can anyone please let me know how to create the topology file. I require 3 
graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd.



The tutorial is indeed outdated but the logic is fairly sound.  You don't have 
to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in 
the working directory and it will override the one at the force field level.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

2014-07-02 Thread Justin Lemkul



On 7/2/14, 10:55 AM, Nikolaos Michelarakis wrote:

Dear Justin,

Thank you very much for your reply. I have tried the converter but I think
I don't have enough experience to get the CHARMM files working properly
with the converter. If I sent you the files, would it be possible to do it
for me or guide me through it?



If you post exactly what you're doing and exactly what the output/error is, I 
might be able to spot the problem.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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[gmx-users] Requesting help on converting a CG (coarse grained) trajectory to a FG (fine grained) trajectory

2014-07-02 Thread Yip Yew Mun
Hi all,

I have just ran a CG MD with the Martini force field, and I was wondering if 
it’s possible to transform this CG trajectory back to a FG trajectory? If it’s 
possible, are there any available tutorials I can follow? If not, please guide 
me on the commands and modules required to execute this action.

Thanks, any help is greatly appreciated. =)

Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry  Biological 
Chemistry
School of Physical  Mathematical Sciences | Nanyang Technological University | 
Singapore 639798
Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sg | GMT+8h

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Re: [gmx-users] Requesting help on converting a CG (coarse grained) trajectory to a FG (fine grained) trajectory

2014-07-02 Thread Justin Lemkul



On 7/2/14, 11:48 AM, Yip Yew Mun wrote:

Hi all,

I have just ran a CG MD with the Martini force field, and I was wondering if 
it’s possible to transform this CG trajectory back to a FG trajectory? If it’s 
possible, are there any available tutorials I can follow? If not, please guide 
me on the commands and modules required to execute this action.



http://md.chem.rug.nl/cgmartini/index.php/others#Reverse-transformation

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] GROMACS 5.0 official release

2014-07-02 Thread Ali Khan
Hey Mark,

This might be a a dumb question, but over the official release download
links on the gromacs website, it still says: Please note that these are
not yet regarded as production quality, pending further testing, but the
code is now feature-stable.

Is this a typo because I thought the official release is production quality.

Best Wishes,
Ali Khan


On Sun, Jun 29, 2014 at 4:53 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi GROMACS users,

 The official release of GROMACS 5.0 is available!

 What new things can you expect?

 * GROMACS now uses a combination of *C++98* and C99, so you will need a
 working C++ compiler that is intended to work with your C compiler


 * Building GROMACS now requires *CMake version 2.8.8*, which will mean some
 of you will need to update your version in order to build GROMACS.

 * The native GPU port available in GROMACS 4.6 supports a wider range of
 simulation types, and now requires CUDA 4.0

 * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
 design principles is that GROMACS will do correct simulations by default,
 and the use of this scheme makes that easy and fast. The group cut-off
 scheme will be removed in a future version, so start planning for that!

 * You can now treat *Lennard-Jones interactions with PME*, which is
 expected to provide a much better treatment of spatially heterogeneous
 long-ranged dispersion interactions at cost comparable to that of a cutoff.
 LJPME is supported for both cut-off schemes, and almost all kinds of
 simullations

 * GROMACS deploys the Random123 stateless random-number generator

 * GROMACS now uses the stochastic dynamics (sd1) integrator of Goga 
 Berendsen

 * GROMACS tools are now bundled together into *just two binaries* - mdrun
 and gmx. The latter contains most of the tools familiar to you, perhaps
 with new names, and a couple of new ones. For the time being, the install
 procedure will also create symbolic links so that your old scripts will
 keep working for a time, but these will go away at some future point!

 * There is support for the new TNG compressed trajectory format

 * GROMACS contains a feature for computational electrophysiology
 simulations, to simulate a steady-state ion concentration difference
 between compartments of a double membrane

 * GROMACS supports some special interactions for coarse-grained
 interactions with Martini force fields

 * GROMACS support for Interactive Molecular Dynamics (IMD)


 * A handful of the tools have been re-implemented using a *new C++ analysis
 framework*, which we hope will provide a better platform for maintaining
 and adding to their functionality in the future.


 * There is an enhanced testing suite, with *unit tests* for most new C++
 code.

 * There is preliminary support for Intel Xeon Phi (only in native mode, and
 performance will only be slightly improved)

 * GROMACS has removed support for particle decomposition - the simulation
 types that required it are now limited to a single MPI rank (but perhaps
 multiple OpenMP threads)

 Please see the link to the release notes below for more details. All the
 content of GROMACS 4.6.6 (whose release is imminent) is present, apart from
 features that have been removed.

 You can find the code, manual, release notes, installation instructions and
 test suite at the links below.

 ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz

 ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf


 http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0

 http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0

 http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz

 Happy simulating!

 Mark Abraham
 GROMACS development manager
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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

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Re: [gmx-users] GROMACS 5.0 official release

2014-07-02 Thread Mark Abraham
On Jul 2, 2014 6:44 PM, Ali Khan ak...@virginia.edu wrote:

 Hey Mark,

 This might be a a dumb question, but over the official release download
 links on the gromacs website, it still says: Please note that these are
 not yet regarded as production quality, pending further testing, but the
 code is now feature-stable.

 Is this a typo because I thought the official release is production
quality.

Indeed, they are. I have fixed my copy-paste error, now. Sorry about that!

Mark
 Best Wishes,
 Ali Khan


 On Sun, Jun 29, 2014 at 4:53 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

  Hi GROMACS users,
 
  The official release of GROMACS 5.0 is available!
 
  What new things can you expect?
 
  * GROMACS now uses a combination of *C++98* and C99, so you will need a
  working C++ compiler that is intended to work with your C compiler
 
 
  * Building GROMACS now requires *CMake version 2.8.8*, which will mean
some
  of you will need to update your version in order to build GROMACS.
 
  * The native GPU port available in GROMACS 4.6 supports a wider range of
  simulation types, and now requires CUDA 4.0
 
  * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
  design principles is that GROMACS will do correct simulations by
default,
  and the use of this scheme makes that easy and fast. The group cut-off
  scheme will be removed in a future version, so start planning for that!
 
  * You can now treat *Lennard-Jones interactions with PME*, which is
  expected to provide a much better treatment of spatially heterogeneous
  long-ranged dispersion interactions at cost comparable to that of a
cutoff.
  LJPME is supported for both cut-off schemes, and almost all kinds of
  simullations
 
  * GROMACS deploys the Random123 stateless random-number generator
 
  * GROMACS now uses the stochastic dynamics (sd1) integrator of Goga 
  Berendsen
 
  * GROMACS tools are now bundled together into *just two binaries* -
mdrun
  and gmx. The latter contains most of the tools familiar to you, perhaps
  with new names, and a couple of new ones. For the time being, the
install
  procedure will also create symbolic links so that your old scripts will
  keep working for a time, but these will go away at some future point!
 
  * There is support for the new TNG compressed trajectory format
 
  * GROMACS contains a feature for computational electrophysiology
  simulations, to simulate a steady-state ion concentration difference
  between compartments of a double membrane
 
  * GROMACS supports some special interactions for coarse-grained
  interactions with Martini force fields
 
  * GROMACS support for Interactive Molecular Dynamics (IMD)
 
 
  * A handful of the tools have been re-implemented using a *new C++
analysis
  framework*, which we hope will provide a better platform for maintaining
  and adding to their functionality in the future.
 
 
  * There is an enhanced testing suite, with *unit tests* for most new C++
  code.
 
  * There is preliminary support for Intel Xeon Phi (only in native mode,
and
  performance will only be slightly improved)
 
  * GROMACS has removed support for particle decomposition - the
simulation
  types that required it are now limited to a single MPI rank (but perhaps
  multiple OpenMP threads)
 
  Please see the link to the release notes below for more details. All the
  content of GROMACS 4.6.6 (whose release is imminent) is present, apart
from
  features that have been removed.
 
  You can find the code, manual, release notes, installation instructions
and
  test suite at the links below.
 
  ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
 
  ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf
 
 
 
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0
 
  http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
 
  http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz
 
  Happy simulating!
 
  Mark Abraham
  GROMACS development manager
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
  send a mail to gmx-users-requ...@gromacs.org.
 
 --
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Re: [gmx-users] [gmx-announce] GROMACS 5.0 official release

2014-07-02 Thread Mark Abraham
Hi,

The warnings are not a problem - gmx view does not get as much love as the
rest of the project!

Mark
On Jul 2, 2014 11:23 AM, Luís Pereira luisp2...@gmail.com wrote:

 Hi,

 Thank you for this new version!

 When compiling we've got these warnings:


  attribute warn_unused_result [-Wunused-result]
   fscanf(in, %6s, buf);
 ^
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:391:28:
  warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
  declared with attribute warn_unused_result [-Wunused-result]
   fscanf(in, %15s, buf);
  ^
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:412:36:
  warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
  declared with attribute warn_unused_result [-Wunused-result]
   fscanf(in, %15s, buf);
  ^
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:416:40:
  warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
  declared with attribute warn_unused_result [-Wunused-result]
   fscanf(in, %15s, buf);
  ^
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:435:36:
  warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
  declared with attribute warn_unused_result [-Wunused-result]
   fscanf(in, %15s, buf);
  ^
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:439:32:
  warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
  declared with attribute warn_unused_result [-Wunused-result]
   fscanf(in, %15s, buf);
  ^
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp: In function
  ‘void ReadAccOpen(const char*, FILE*)’:
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:106:27:
  warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
  declared with attribute warn_unused_result [-Wunused-result]
   fscanf(in, %4s, buf);
 ^
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp: In function
  ‘void ReadAccClose(const char*, FILE*)’:
  /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:117:27:
  warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’,
  declared with attribute warn_unused_result [-Wunused-result]
   fscanf(in, %4s, buf);
 ^


 OS is ubuntu 14.04 64 bit, virtualbox machine:

 GROMACS:  gmx, VERSION 5.0
  Executable:   /usr/local/gromacs/bin/gmx
  Library dir:  /usr/local/gromacs/share/gromacs/top
  Command line:
gmx -version
  Gromacs version:VERSION 5.0
  Precision:  single
  Memory model:   64 bit
  MPI library:thread_mpi
  OpenMP support: enabled
  GPU support:disabled
  invsqrt routine:gmx_software_invsqrt(x)
  SIMD instructions:  SSE2
  FFT library:fftw-3.3.3-sse2-avx
  RDTSCP usage:   enabled
  C++11 compilation:  enabled
  TNG support:enabled
  Tracing support:disabled
  Built on:   Qua Jul  2 09:54:48 WEST 2014
  Built by:   arh@arh-VirtualBox [CMAKE]
  Build OS/arch:  Linux 3.13.0-24-generic x86_64
  Build CPU vendor:   GenuineIntel
  Build CPU brand:Intel(R) Xeon(R) CPU   E5530  @ 2.40GHz
  Build CPU family:   6   Model: 26   Stepping: 5
  Build CPU features: apic clfsh cmov cx8 lahf_lm mmx msr pse rdtscp sse2
  sse3 ssse3
  C compiler: /usr/bin/cc GNU 4.8.2
  C compiler flags:-msse2   -Wno-maybe-uninitialized -Wextra
  -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
  -Wno-unused -Wunused-value -Wunused-parameter   -fomit-frame-pointer
  -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds  -O3
 -DNDEBUG
  C++ compiler:   /usr/bin/c++ GNU 4.8.2
  C++ compiler flags:  -msse2   -std=c++0x -Wextra
  -Wno-missing-field-initializers -Wpointer-arith -Wall
 -Wno-unused-function
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast
   -Wno-array-bounds  -O3 -DNDEBUG
  Boost version:  1.55.0 (internal)




 On 29 June 2014 21:53, Mark Abraham mark.j.abra...@gmail.com wrote:

  Hi GROMACS users,
 
  The official release of GROMACS 5.0 is available!
 
  What new things can you expect?
 
  * GROMACS now uses a combination of *C++98* and C99, so you will need a
  working C++ compiler that is intended to work with your C compiler
 
 
  * Building GROMACS now requires *CMake version 2.8.8*, which will mean
  some of you will need to update your version in order to build GROMACS.
 
  * The native GPU port available in GROMACS 4.6 supports a wider range of
  simulation types, and now requires CUDA 4.0
 
  * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
  design principles is that GROMACS will do correct simulations by default,
  and the 

Re: [gmx-users] Regarding lipid topology

2014-07-02 Thread Venkat Reddy
Thank you Sir. Sorry for the late reply. So, the changes like dihedral
angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
there any other adjustments I should make to build the trans lipid isomer
topology from cis? Thank you for your valuable time and concern.


On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban vvcha...@gmail.com
wrote:

 Of course, no. You need to adjust your topology (force field?) to
 distinguish between cis- and trans- states.


 Dr. Vitaly V. Chaban


 On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy venkat...@gmail.com
 wrote:
  Dear all,
  I want to simulate a membrane protein system. My membrane is composed of
  DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC
 topology
  from lipidbook website. Since DOPC and DEPC are isomers, can I use the
  topology of DOPC for DEPC also?
 
  Thank and regards
 
  Venkat Reddy Chirasani
  PhD student
  Laboratory of Computational Biophysics
  Department of Biotechnology
  IIT Madras
  Chennai
  INDIA-600036
  --
  Gromacs Users mailing list
 
  * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
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 send a mail to gmx-users-requ...@gromacs.org.
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 send a mail to gmx-users-requ...@gromacs.org.




-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] Gromacs 5.0 download

2014-07-02 Thread Harshkumar Singh
I know this is a silly question but in the downloads section when I click
to download it the new window opens and 0bit tar file is downloaded.I
switched to windows but even then the new tab doesn't show anything.I don't
understand why is this happening.
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Re: [gmx-users] Gromacs 5.0 download

2014-07-02 Thread Szilárd Páll
The link is correct, something must be broken on your side. Try using e.g. wget:

$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz  ls -l gromacs*.gz
--2014-07-02 22:34:44--  ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
   = `gromacs-5.0.tar.gz'
Resolving ftp.gromacs.org... 130.238.41.205
Connecting to ftp.gromacs.org|130.238.41.205|:21... connected.
Logging in as anonymous ... Logged in!
== SYST ... done.== PWD ... done.
== TYPE I ... done.  == CWD (1) /pub/gromacs ... done.
== SIZE gromacs-5.0.tar.gz ... 26862408
== PASV ... done.== RETR gromacs-5.0.tar.gz ... done.
Length: 26862408 (26M) (unauthoritative)

100%[]
26,862,408  28.6M/s   in 0.9s

2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408]

Cheers,
--
Szilárd


On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh
harshsingh2...@gmail.com wrote:
 I know this is a silly question but in the downloads section when I click
 to download it the new window opens and 0bit tar file is downloaded.I
 switched to windows but even then the new tab doesn't show anything.I don't
 understand why is this happening.
 --
 Gromacs Users mailing list

 * Please search the archive at 
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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

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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
 mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Gromacs 5.0 download

2014-07-02 Thread Roland Schulz
Maybe something on your end is blocking ftp connections. You can download
from a mirror such as:
http://fossies.org/linux/privat/gromacs-5.0.tar.gz
If you download from a mirror make sure to check the md5sum.


On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll pall.szil...@gmail.com wrote:

 The link is correct, something must be broken on your side. Try using e.g.
 wget:

 $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz  ls -l
 gromacs*.gz
 --2014-07-02 22:34:44--
 ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
= `gromacs-5.0.tar.gz'
 Resolving ftp.gromacs.org... 130.238.41.205
 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected.
 Logging in as anonymous ... Logged in!
 == SYST ... done.== PWD ... done.
 == TYPE I ... done.  == CWD (1) /pub/gromacs ... done.
 == SIZE gromacs-5.0.tar.gz ... 26862408
 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done.
 Length: 26862408 (26M) (unauthoritative)

 100%[]
 26,862,408  28.6M/s   in 0.9s

 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408]

 Cheers,
 --
 Szilárd


 On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh
 harshsingh2...@gmail.com wrote:
  I know this is a silly question but in the downloads section when I click
  to download it the new window opens and 0bit tar file is downloaded.I
  switched to windows but even then the new tab doesn't show anything.I
 don't
  understand why is this happening.
  --
  Gromacs Users mailing list
 
  * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.
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 posting!

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 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.




-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Gromacs 5.0 download

2014-07-02 Thread Harshkumar Singh
Yeah apparently the ftp connection is blocked.I actually forgot that.Thanks
for the help.


On Thu, Jul 3, 2014 at 2:16 AM, Roland Schulz rol...@utk.edu wrote:

 Maybe something on your end is blocking ftp connections. You can download
 from a mirror such as:
 http://fossies.org/linux/privat/gromacs-5.0.tar.gz
 If you download from a mirror make sure to check the md5sum.


 On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll pall.szil...@gmail.com
 wrote:

  The link is correct, something must be broken on your side. Try using
 e.g.
  wget:
 
  $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz  ls -l
  gromacs*.gz
  --2014-07-02 22:34:44--
  ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
 = `gromacs-5.0.tar.gz'
  Resolving ftp.gromacs.org... 130.238.41.205
  Connecting to ftp.gromacs.org|130.238.41.205|:21... connected.
  Logging in as anonymous ... Logged in!
  == SYST ... done.== PWD ... done.
  == TYPE I ... done.  == CWD (1) /pub/gromacs ... done.
  == SIZE gromacs-5.0.tar.gz ... 26862408
  == PASV ... done.== RETR gromacs-5.0.tar.gz ... done.
  Length: 26862408 (26M) (unauthoritative)
 
 
 100%[]
  26,862,408  28.6M/s   in 0.9s
 
  2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408]
 
  Cheers,
  --
  Szilárd
 
 
  On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh
  harshsingh2...@gmail.com wrote:
   I know this is a silly question but in the downloads section when I
 click
   to download it the new window opens and 0bit tar file is downloaded.I
   switched to windows but even then the new tab doesn't show anything.I
  don't
   understand why is this happening.
   --
   Gromacs Users mailing list
  
   * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
  
   * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  
   * For (un)subscribe requests visit
   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
  send a mail to gmx-users-requ...@gromacs.org.
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
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  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
  send a mail to gmx-users-requ...@gromacs.org.
 



 --
 ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
 865-241-1537, ORNL PO BOX 2008 MS6309
 --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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-- 
Harshkumar Singh
2nd Year Integrated MSc Chemistry
IIT Bombay.
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[gmx-users] g_polystat sorts the eigen vector

2014-07-02 Thread Chandan Choudhury
Dear gmx users,

The g_polystat tool arranges the Rg eigen vectors in the descending order.
We cannot see how a particular eigen vector (one along the X-axis) varies
with time. We can obviously comment the section of the g_polystat code to
avoid the sorting. Is there a reason, why do we sort the eigen vectors? It
would be helpful if someone help me to understand this.

Thanks
Chandan

--
Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India
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Re: [gmx-users] Gromacs 5.0 download

2014-07-02 Thread Justin Lemkul



On 7/2/14, 4:36 PM, Szilárd Páll wrote:

The link is correct, something must be broken on your side. Try using e.g. wget:

$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz  ls -l gromacs*.gz
--2014-07-02 22:34:44--  ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
= `gromacs-5.0.tar.gz'
Resolving ftp.gromacs.org... 130.238.41.205
Connecting to ftp.gromacs.org|130.238.41.205|:21... connected.
Logging in as anonymous ... Logged in!
== SYST ... done.== PWD ... done.
== TYPE I ... done.  == CWD (1) /pub/gromacs ... done.
== SIZE gromacs-5.0.tar.gz ... 26862408
== PASV ... done.== RETR gromacs-5.0.tar.gz ... done.
Length: 26862408 (26M) (unauthoritative)

100%[]
26,862,408  28.6M/s   in 0.9s



I'm having a similar problem as the OP.  The web interface just seems to hang 
and using wget takes over an hour with a download rate of  4 KB/sec.  This is 
true at work (hardwired workstation) and at home (laptop on wifi)


-Justin


2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408]

Cheers,
--
Szilárd


On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh
harshsingh2...@gmail.com wrote:

I know this is a silly question but in the downloads section when I click
to download it the new window opens and 0bit tar file is downloaded.I
switched to windows but even then the new tab doesn't show anything.I don't
understand why is this happening.
--
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--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Gromacs 5.0 download

2014-07-02 Thread Szilárd Páll
On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:


 On 7/2/14, 4:36 PM, Szilárd Páll wrote:

 The link is correct, something must be broken on your side. Try using e.g.
 wget:

 $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz  ls -l
 gromacs*.gz
 --2014-07-02 22:34:44--
 ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
 = `gromacs-5.0.tar.gz'
 Resolving ftp.gromacs.org... 130.238.41.205
 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected.
 Logging in as anonymous ... Logged in!
 == SYST ... done.== PWD ... done.
 == TYPE I ... done.  == CWD (1) /pub/gromacs ... done.
 == SIZE gromacs-5.0.tar.gz ... 26862408
 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done.
 Length: 26862408 (26M) (unauthoritative)


 100%[]
 26,862,408  28.6M/s   in 0.9s


 I'm having a similar problem as the OP.  The web interface just seems to
 hang and using wget takes over an hour with a download rate of  4 KB/sec.
 This is true at work (hardwired workstation) and at home (laptop on wifi)

OK, that's alarming. Perhaps uu.se (which hosts ftp.gromacs.org) got
hit hard by the downloads and they throttle (some) connections. Note
mine, though, as you can see I got a 28.6 M/s average download speed
(but that's of course an unfair comparison).

Not sure how to check whether the downloads are really being
throttled, but perhaps we should use an alternative host or torrent.

 -Justin


 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408]

 Cheers,
 --
 Szilárd


 On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh
 harshsingh2...@gmail.com wrote:

 I know this is a silly question but in the downloads section when I click
 to download it the new window opens and 0bit tar file is downloaded.I
 switched to windows but even then the new tab doesn't show anything.I
 don't
 understand why is this happening.
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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 send a mail to gmx-users-requ...@gromacs.org.


 --
 ==

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

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

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

 ==

 --
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Re: [gmx-users] obtaining .gro timeframe

2014-07-02 Thread Chetan Mahajan
Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be seen in the following snapshot? I would
expect many of them scattered in space, beyond original box?

https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va

Dark blue line is the box boundary.

Thanks
Chetan


On Wed, Jul 2, 2014 at 5:14 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/1/14, 11:28 PM, Chetan Mahajan wrote:

 Thanks, Justin. *Until now, I was thinking that xtc coordinates are

 wrapped. It's good to know that coordinates from xtc files are unwrapped
 (please comment if not correct, since we talked only with respect to gro


 That is correct.  mdrun doesn't care about our visualization convenience.
  No sense in wasting performance doing imaging on the fly when it's not
 necessary.

  file). *But I am confused at another thing. I have known at the origin of
 the box is at one of its vertices ( is that not true?). *Then why are some

 coordinates in .gro file (the one generated at the end of gromacs MD run)
 negative, if coordinates are wrapped in the box?*


 Molecules are made whole; sometimes they're translated in the positive
 direction, sometimes in the negative direction, depending on how the
 molecule is being reconstructed.


  Is my original command using trjconv okay?


 OK is relative.  In this case, you seem troubled by the slight
 difference in convention, but there's nothing wrong with the command.  If
 you want trjconv to make molecules whole, use -pbc mol or -pbc whole.  Your
 original command simply dumps the coordinates and does nothing about
 periodicity.

  Whereas I do get a sample x-coordinate in .gro file, generated at the end
 of MD run (let's call it gro1) from that in .gro file, generated using
 trjconv on xtc (let's call it gro2) by adding a box length to concerned
 coordinate in gro2, (as shown in excerpt 1) , it's only by subtracting a
 boxlength that we interconvert between similar values, as shown in excerpt
 2 of the SAME file. *Why is there no consistency of conversion between
 SAME

 two .gro files for all the coordinates? How do I mathematically obtain
 file
 2 from file 1 with some consistent measure?  *


 See above.  trjconv will do it for you.

 -Justin

  - : for .gro file at the end of gromacs MD run (gro1)
 + : for .gro timeframe file obtained from .xtc trajectory ( using trjconv)
 (gro2)

 *EXCERT 1*


 -   11SOLHW1 2188   3.244   3.071  10.934
 -   11SOLHW2 2189   3.211   2.940  10.842
 +   11SOLHW1 2188   0.023   3.071  10.934
 +   11SOLHW2 2189  -0.011   2.940  10.842


 *EXCERT 2*

 -   56SOLHW1 2323  -0.031   1.076   1.130
 -   56SOLHW2 2324  -0.040   1.096   1.292
 +   56SOLHW1 2323   3.191   1.076   1.130
 +   56SOLHW2 2324   3.182   1.096   1.292

 Thanks
 Chetan

 On Tue, Jul 1, 2014 at 8:10 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 7/1/14, 9:08 PM, Chetan Mahajan wrote:

  Thanks, Justin. Are you saying, the coordinates in .gro  file extracted
 from xtc trajectory are not wrapped, whereas those in the .gro file
 generated at the end of gromacs MD run are wrapped in the box?


  Yes, unless you've manipulated the trajectory in some way with trjconv
 beforehand.


   Now I have a question:  the negative coordinates that are present in
 the

 following text are from .gro file (generated at the end of MD run),
 whereas
 positive ones are from .gro file obtained using trjconv on xtc.


  Either way, it's a periodicity effect.  Molecules are made whole.


 -Justin

 --
 ==

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

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

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

 ==
 --
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 * Please search the archive at http://www.gromacs.org/
 Support/Mailing_Lists/GMX-Users_List before posting!

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 send a mail to gmx-users-requ...@gromacs.org.


 --
 ==

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

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

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

 ==
 --
 Gromacs Users mailing list

 * Please search the 

Re: [gmx-users] obtaining .gro timeframe

2014-07-02 Thread Justin Lemkul



On 7/2/14, 6:45 PM, Chetan Mahajan wrote:

Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be seen in the following snapshot? I would
expect many of them scattered in space, beyond original box?

https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va

Dark blue line is the box boundary.



A central unit cell is still maintained; it's just that the molecules aren't 
necessarily whole.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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Re: [gmx-users] Gromacs 5.0 download

2014-07-02 Thread Harshkumar Singh
I ran the md5sum but it does not match with any of the hashes.What should I
do now?


On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll pall.szil...@gmail.com wrote:

 On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:
 
 
  On 7/2/14, 4:36 PM, Szilárd Páll wrote:
 
  The link is correct, something must be broken on your side. Try using
 e.g.
  wget:
 
  $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz  ls -l
  gromacs*.gz
  --2014-07-02 22:34:44--
  ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
  = `gromacs-5.0.tar.gz'
  Resolving ftp.gromacs.org... 130.238.41.205
  Connecting to ftp.gromacs.org|130.238.41.205|:21... connected.
  Logging in as anonymous ... Logged in!
  == SYST ... done.== PWD ... done.
  == TYPE I ... done.  == CWD (1) /pub/gromacs ... done.
  == SIZE gromacs-5.0.tar.gz ... 26862408
  == PASV ... done.== RETR gromacs-5.0.tar.gz ... done.
  Length: 26862408 (26M) (unauthoritative)
 
 
 
 100%[]
  26,862,408  28.6M/s   in 0.9s
 
 
  I'm having a similar problem as the OP.  The web interface just seems to
  hang and using wget takes over an hour with a download rate of  4
 KB/sec.
  This is true at work (hardwired workstation) and at home (laptop on wifi)

 OK, that's alarming. Perhaps uu.se (which hosts ftp.gromacs.org) got
 hit hard by the downloads and they throttle (some) connections. Note
 mine, though, as you can see I got a 28.6 M/s average download speed
 (but that's of course an unfair comparison).

 Not sure how to check whether the downloads are really being
 throttled, but perhaps we should use an alternative host or torrent.

  -Justin
 
 
  2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408]
 
  Cheers,
  --
  Szilárd
 
 
  On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh
  harshsingh2...@gmail.com wrote:
 
  I know this is a silly question but in the downloads section when I
 click
  to download it the new window opens and 0bit tar file is downloaded.I
  switched to windows but even then the new tab doesn't show anything.I
  don't
  understand why is this happening.
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
  send a mail to gmx-users-requ...@gromacs.org.
 
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 601
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
 
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
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 send a
  mail to gmx-users-requ...@gromacs.org.
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 send a mail to gmx-users-requ...@gromacs.org.




-- 
Harshkumar Singh
2nd Year Integrated MSc Chemistry
IIT Bombay.
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[gmx-users] Solvating protein in a CG representation - genbox problem

2014-07-02 Thread Carlos Navarrro Retamal
Dear gromacs users,  
I’m following this tutorial - 
http://md.chem.rug.nl/cgmartini/index.php/proteins
in order to performed a CG simulation of an specific protein in a water box.
My problem is that when i’m trying to solvate my protein with genbox, by using 
the next command:

 genbox -cp COR15A_CG-box.gro -cs water-box-303K-1bar.gro -vdwd 0.21 -o 
 COR15A_CG-solvated.gro
  

The water box is placed next to the protein instead of surrounding it- 
http://cl.ly/1U2F1H3y3n2w.
I used the following command to center my protein before i used genbox, without 
luck :/

 editconf -f COR15A_CG.pdb -center 0 0 0 -o COR15A_CG-box.gro -c -d 2.0 -bt 
 cubic
I’m just start by using a CG representation of biological systems, so any help 
will be welcome.
Have a nice day,
Carlos  


--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl

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Re: [gmx-users] Gromacs 5.0 download

2014-07-02 Thread Roland Schulz
On Wed, Jul 2, 2014 at 6:55 PM, Harshkumar Singh harshsingh2...@gmail.com
wrote:

 I ran the md5sum but it does not match with any of the hashes.What should I
 do now?


Which file from which server (/which URL) did you download? What md5 did
you get?

Roland




 On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll pall.szil...@gmail.com
 wrote:

  On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:
  
  
   On 7/2/14, 4:36 PM, Szilárd Páll wrote:
  
   The link is correct, something must be broken on your side. Try using
  e.g.
   wget:
  
   $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz  ls -l
   gromacs*.gz
   --2014-07-02 22:34:44--
   ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
   = `gromacs-5.0.tar.gz'
   Resolving ftp.gromacs.org... 130.238.41.205
   Connecting to ftp.gromacs.org|130.238.41.205|:21... connected.
   Logging in as anonymous ... Logged in!
   == SYST ... done.== PWD ... done.
   == TYPE I ... done.  == CWD (1) /pub/gromacs ... done.
   == SIZE gromacs-5.0.tar.gz ... 26862408
   == PASV ... done.== RETR gromacs-5.0.tar.gz ... done.
   Length: 26862408 (26M) (unauthoritative)
  
  
  
 
 100%[]
   26,862,408  28.6M/s   in 0.9s
  
  
   I'm having a similar problem as the OP.  The web interface just seems
 to
   hang and using wget takes over an hour with a download rate of  4
  KB/sec.
   This is true at work (hardwired workstation) and at home (laptop on
 wifi)
 
  OK, that's alarming. Perhaps uu.se (which hosts ftp.gromacs.org) got
  hit hard by the downloads and they throttle (some) connections. Note
  mine, though, as you can see I got a 28.6 M/s average download speed
  (but that's of course an unfair comparison).
 
  Not sure how to check whether the downloads are really being
  throttled, but perhaps we should use an alternative host or torrent.
 
   -Justin
  
  
   2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved
 [26862408]
  
   Cheers,
   --
   Szilárd
  
  
   On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh
   harshsingh2...@gmail.com wrote:
  
   I know this is a silly question but in the downloads section when I
  click
   to download it the new window opens and 0bit tar file is downloaded.I
   switched to windows but even then the new tab doesn't show anything.I
   don't
   understand why is this happening.
   --
   Gromacs Users mailing list
  
   * Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
  
   * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  
   * For (un)subscribe requests visit
   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
   send a mail to gmx-users-requ...@gromacs.org.
  
  
   --
   ==
  
   Justin A. Lemkul, Ph.D.
   Ruth L. Kirschstein NRSA Postdoctoral Fellow
  
   Department of Pharmaceutical Sciences
   School of Pharmacy
   Health Sciences Facility II, Room 601
   University of Maryland, Baltimore
   20 Penn St.
   Baltimore, MD 21201
  
   jalem...@outerbanks.umaryland.edu | (410) 706-7441
   http://mackerell.umaryland.edu/~jalemkul
  
   ==
  
   --
   Gromacs Users mailing list
  
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 --
 Harshkumar Singh
 2nd Year Integrated MSc Chemistry
 IIT Bombay.
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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Solvating protein in a CG representation - genbox roblem

2014-07-02 Thread Carlos Navarrro Retamal
Never mind.
I used editconf before the energy-minimisation on vacuum (specifying the 
size-box) and now, when i used genbox on the ’new’ structured it worked :D

   

--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Wednesday, July 2, 2014 at 8:56 PM, Carlos Navarrro Retamal wrote:

 Dear gromacs users,  
 I’m following this tutorial - 
 http://md.chem.rug.nl/cgmartini/index.php/proteins
 in order to performed a CG simulation of an specific protein in a water box.
 My problem is that when i’m trying to solvate my protein with genbox, by 
 using the next command:
  
  genbox -cp COR15A_CG-box.gro -cs water-box-303K-1bar.gro -vdwd 0.21 -o 
  COR15A_CG-solvated.gro
   
   
  
  
 The water box is placed next to the protein instead of surrounding it- 
 http://cl.ly/1U2F1H3y3n2w.
 I used the following command to center my protein before i used genbox, 
 without luck :/
  
  editconf -f COR15A_CG.pdb -center 0 0 0 -o COR15A_CG-box.gro -c -d 2.0 -bt 
  cubic
 I’m just start by using a CG representation of biological systems, so any 
 help will be welcome.
 Have a nice day,
 Carlos  
  
  
 --  
 Carlos Navarro Retamal
 Bioinformatic engineer
 Ph.D(c) in Applied Science, Universidad de Talca, Chile
 Center of Bioinformatics and Molecular Simulations (CBSM)
 Universidad de Talca
 2 Norte 685, Casilla 721, Talca - Chile  
 Teléfono: 56-71-201 798,  
 Fax: 56-71-201 561
 Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or 
 cnava...@utalca.cl (mailto:cnava...@utalca.cl)
  
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[gmx-users] regarding error during EM

2014-07-02 Thread dhaval patel
*Fatal error:*
25 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
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Re: [gmx-users] Graphene topology file

2014-07-02 Thread #SUKRITI GUPTA#
Dear Justin,

Thanks for the reply but I am writing the .n2t file still getting the error 
that Could not find force field 'graphite_oplsaa' in current directory, 
install tree or GMXDATA path. What should I do? Moreover i don't think that 
n2t file tells program to use graphite_oplsaa force field. 

Regards
Sukriti



Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, 
Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul 
jalem...@vt.edu
Sent: Wednesday, July 2, 2014 11:29 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Graphene topology file

On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
 Dear all,


 I want to simulate graphite in water, for which i am trying to create a 
 topology file for graphite. As its .rtp file cannot be written correctly, i 
 tried to use g_x2top command following the steps given in following tutorial.

 http://chembytes.wikidot.com/grocnt


 But I think this tutorial is quite old and hence suitable for older version 
 of gromacs as it still uses FF.dat file. Moreover if i am trying to make a 
 new forcefield directory with name graphite_oplsaa containing the modified 
 files like .n2t,.rtp and .itp, its giving me an error that Could not find 
 force field 'graphite_oplsaa' in current directory, install tree or GMXDATA 
 path. When I try to add this forcefield in original path ie. 
 user/share/gromacs/top, it does not allow me to do that as i am not the 
 administrator. Can anyone please let me know how to create the topology file. 
 I require 3 graphene sheets with pbc. I have created the .pdb file using 
 nanobuilder in vmd.


The tutorial is indeed outdated but the logic is fairly sound.  You don't have
to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in
the working directory and it will override the one at the force field level.

-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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[gmx-users] conf.gro

2014-07-02 Thread RINU KHATTRI
hello gromacs users
i am working on protein ligand compex with popc membrane for ligand
prepration from where i can get conf.gro file
because i am using conf.gro file from gromacs folder (tutor folder -water )
gromacs 4.5.7.
kindly help
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