Re: [gmx-users] Re: charge group in topology file

[David van der Spoel]

[EMAIL PROTECTED] wrote:

Hi,
All

I am running gromacs for simulation of 5 peptides. I have a problem with
the topology file in which the charge on each and every charge group is
not coming whole but in some of them it is in fraction which is not
correct. I have used G43a1 as well as OPLS but i am getting the same
problem with both of them. Now i don't know how to deal with it.
here is the part of topology file after pdb2gmx -f 1st.pdb -p 1st.top -o
1st.gro


in the example below the charge is integer after every residue. See 
column with qtot.




Can anyone help me.
Thanks in Advance
ALKA

[ moleculetype ]
; Namenrexcl
Protein 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
 1   opls_287  1GLY  N  1   -0.314.0067   ;
qtot -0.3
 2   opls_290  1GLY H1  1   0.33  1.008   ;
qtot 0.03
 3   opls_290  1GLY H2  1   0.33  1.008   ;
qtot 0.36
 4   opls_290  1GLY H3  1   0.33  1.008   ;
qtot 0.69
 5  opls_292B  1GLY CA  1   0.19 12.011   ;
qtot 0.88
 6   opls_140  1GLYHA1  1   0.06  1.008   ;
qtot 0.94
 7   opls_140  1GLYHA2  1   0.06  1.008   ;
qtot 1
 8   opls_235  1GLY  C  20.5 12.011   ;
qtot 1.5
 9   opls_236  1GLY  O  2   -0.515.9994   ;
qtot 1
10   opls_238  2ASN  N  3   -0.514.0067   ;
qtot 0.5
11   opls_241  2ASN  H  30.3  1.008   ;
qtot 0.8
12  opls_224B  2ASN CA  4   0.14 12.011   ;
qtot 0.94
13   opls_140  2ASN HA  4   0.06  1.008   ;
qtot 1
14   opls_136  2ASN CB  5  -0.12 12.011   ;
qtot 0.88
15   opls_140  2ASNHB1  5   0.06  1.008   ;
qtot 0.94
16   opls_140  2ASNHB2  5   0.06  1.008   ;
qtot 1
17   opls_235  2ASN CG  60.5 12.011   ;
qtot 1.5
18   opls_236  2ASNOD1  6   -0.515.9994   ;
qtot 1
19   opls_237  2ASNND2  7  -0.7614.0067   ;
qtot 0.24
20   opls_240  2ASN   HD21  7   0.38  1.008   ;
qtot 0.62
21   opls_240  2ASN   HD22  7   0.38  1.008   ;
qtot 1
22   opls_235  2ASN  C  80.5 12.011   ;
qtot 1.5
23   opls_236  2ASN  O  8   -0.515.9994   ;
qtot 1
24   opls_238  3ASN  N  9   -0.514.0067   ;
qtot 0.5
25   opls_241  3ASN  H  90.3  1.008   ;
qtot 0.8
26  opls_224B  3ASN CA 10   0.14 12.011   ;
qtot 0.94
27   opls_140  3ASN HA 10   0.06  1.008   ;
qtot 1
28   opls_136  3ASN CB 11  -0.12 12.011   ;
qtot 0.88


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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Diffusion Cofficient of POPC

[David van der Spoel]

minnale wrote:
 
Hi all,
I have read the literature about Diffusion cofficient(Dynamics in 
atomistic simulations of phospholipid membranes: Nuclear magnetic 
resonance relaxation rates and lateral diffusion, Vol-125, page-204703, 
Journal-THE JOURNAL OF CHEMICAL PHYSICS)

then I have given command like this
g_msd -f 5ns_popc.xtc -s .tpr -n p4.ndx -o msd_popc.xvg -lateral z
In the index file i have selceted p8 for the centre of mass and it will 
be  like this

[ P8 ]
  8  60  112  164 ..

I got the diffusion cofficient value like this
MSD gathered over 5000 ps with 501 restarts
# Diffusion constants fitted from time 500 to 4500 ps
# D[P8] = 0.0131 (+/- 0.0190) (1e-5 cm^2/s)

The actual D=(1-10)*10-7 cm2/s from above mentioned article but iam 
getting the value 1e-5 cm^2/s


Aren't you getting 0.0131e-5 = 1.31e-7?



I have tried in different ways with options -type z but I didnt get the 
value near to actual value.


Could you please tell me where I am doing mistake

Thanks alot in advance.



Rediff Shopping 






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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] Re: charge group in topology file

[alkasrivastava]

Hi,
All

I am running gromacs for simulation of 5 peptides. I have a problem with
the topology file in which the charge on each and every charge group is
not coming whole but in some of them it is in fraction which is not
correct. I have used G43a1 as well as OPLS but i am getting the same
problem with both of them. Now i don't know how to deal with it.
here is the part of topology file after pdb2gmx -f 1st.pdb -p 1st.top -o
1st.gro

Can anyone help me.
Thanks in Advance
ALKA

[ moleculetype ]
; Namenrexcl
Protein 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
 1   opls_287  1GLY  N  1   -0.314.0067   ;
qtot -0.3
 2   opls_290  1GLY H1  1   0.33  1.008   ;
qtot 0.03
 3   opls_290  1GLY H2  1   0.33  1.008   ;
qtot 0.36
 4   opls_290  1GLY H3  1   0.33  1.008   ;
qtot 0.69
 5  opls_292B  1GLY CA  1   0.19 12.011   ;
qtot 0.88
 6   opls_140  1GLYHA1  1   0.06  1.008   ;
qtot 0.94
 7   opls_140  1GLYHA2  1   0.06  1.008   ;
qtot 1
 8   opls_235  1GLY  C  20.5 12.011   ;
qtot 1.5
 9   opls_236  1GLY  O  2   -0.515.9994   ;
qtot 1
10   opls_238  2ASN  N  3   -0.514.0067   ;
qtot 0.5
11   opls_241  2ASN  H  30.3  1.008   ;
qtot 0.8
12  opls_224B  2ASN CA  4   0.14 12.011   ;
qtot 0.94
13   opls_140  2ASN HA  4   0.06  1.008   ;
qtot 1
14   opls_136  2ASN CB  5  -0.12 12.011   ;
qtot 0.88
15   opls_140  2ASNHB1  5   0.06  1.008   ;
qtot 0.94
16   opls_140  2ASNHB2  5   0.06  1.008   ;
qtot 1
17   opls_235  2ASN CG  60.5 12.011   ;
qtot 1.5
18   opls_236  2ASNOD1  6   -0.515.9994   ;
qtot 1
19   opls_237  2ASNND2  7  -0.7614.0067   ;
qtot 0.24
20   opls_240  2ASN   HD21  7   0.38  1.008   ;
qtot 0.62
21   opls_240  2ASN   HD22  7   0.38  1.008   ;
qtot 1
22   opls_235  2ASN  C  80.5 12.011   ;
qtot 1.5
23   opls_236  2ASN  O  8   -0.515.9994   ;
qtot 1
24   opls_238  3ASN  N  9   -0.514.0067   ;
qtot 0.5
25   opls_241  3ASN  H  90.3  1.008   ;
qtot 0.8
26  opls_224B  3ASN CA 10   0.14 12.011   ;
qtot 0.94
27   opls_140  3ASN HA 10   0.06  1.008   ;
qtot 1
28   opls_136  3ASN CB 11  -0.12 12.011   ;
qtot 0.88


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Re: [gmx-users] Diffusion Cofficient of POPC

[Jojart Balazs]

Dear Minnale,
As far as i know, at least 100ns simulation should be performed in order 
to obtain the correct diffusion coefficient for lipids. I think, if you 
performed 5 ns it is too short.

Hope this helps.
balazs

minnale wrote:


 
Hi all,
I have read the literature about Diffusion cofficient(Dynamics in 
atomistic simulations of phospholipid membranes: Nuclear magnetic 
resonance relaxation rates and lateral diffusion, Vol-125, 
page-204703, Journal-THE JOURNAL OF CHEMICAL PHYSICS)

then I have given command like this
g_msd -f 5ns_popc.xtc -s .tpr -n p4.ndx -o msd_popc.xvg -lateral z
In the index file i have selceted p8 for the centre of mass and it 
will be  like this

[ P8 ]
  8  60  112  164 ..

I got the diffusion cofficient value like this
MSD gathered over 5000 ps with 501 restarts
# Diffusion constants fitted from time 500 to 4500 ps
# D[P8] = 0.0131 (+/- 0.0190) (1e-5 cm^2/s)

The actual D=(1-10)*10-7 cm2/s from above mentioned article but iam 
getting the value 1e-5 cm^2/s


I have tried in different ways with options -type z but I didnt get 
the value near to actual value.


Could you please tell me where I am doing mistake

Thanks alot in advance.



Rediff Shopping 
 



No virus found in this incoming message.
Checked by AVG - http://www.avg.com 
Version: 8.0.138 / Virus Database: 270.4.11/1553 - Release Date: 15/07/2008 05:48
  



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[gmx-users] Diffusion Cofficient of POPC

[minnale]

  
Hi all, 
 I have read the literature about Diffusion cofficient(Dynamics in 
atomistic simulations of phospholipid membranes: Nuclear magnetic resonance 
relaxation rates and lateral diffusion, Vol-125, page-204703, Journal-THE 
JOURNAL OF CHEMICAL PHYSICS)
then I have given command like this
 g_msd -f 5ns_popc.xtc -s .tpr -n p4.ndx -o msd_popc.xvg -lateral z
In the index file i have selceted p8 for the centre of mass and it will be  
like this
[ P8 ]
   8   60  112  164 ..

I got the diffusion cofficient value like this 
MSD gathered over 5000 ps with 501 restarts
# Diffusion constants fitted from time 500 to 4500 ps
# D[P8] = 0.0131 (+/- 0.0190) (1e-5 cm^2/s) 

The actual D=(1-10)*10-7 cm2/s from above mentioned article but iam getting the 
value 1e-5 cm^2/s

I have tried in different ways with options -type z but I didnt get the value 
near to actual value.

Could you please tell me where I am doing mistake 

Thanks alot in advance.___
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Re: [gmx-users] help

[Justin A. Lemkul]

[EMAIL PROTECTED] wrote:

Hi,
I am trying to simulate a protein with a DPC micelle. Part of pdb files is:

CRYST10.0000.0000.000  90.00  90.00  90.00 P 1   1
ATOM  1  N   DPC M   1 -16.481  21.283  -0.739  1.00  0.00  MICE
ATOM  2  C14 DPC M   1 -15.620  20.082  -1.136  1.00  0.00  MICE
ATOM  3  C15 DPC M   1 -17.727  20.772  -0.234  1.00  0.00  MICE
ATOM  4  C16 DPC M   1 -15.792  22.061   0.317  1.00  0.00  MICE
ATOM  5  C17 DPC M   1 -16.780  22.230  -1.919  1.00  0.00  MICE
ATOM  6 H141 DPC M   1 -14.613  20.409  -1.348  1.00  0.00  MICE
ATOM  7 H142 DPC M   1 -16.000  19.717  -2.079  1.00  0.00  MICE
ATOM  8 H151 DPC M   1 -18.375  21.592   0.038  1.00  0.00  MICE
ATOM  9 H152 DPC M   1 -17.513  20.198   0.656  1.00  0.00  MICE

But when I use the command pdb2gmx, it is said "Residue 'DPC' not found 
in residue topology database". How can I deal with it? Thank you.


This is probably the most common question asked on this list.  As such, when 
encountering problems, please do the following:


1. Search the list archive (www.gromacs.org, click "Search")
2. Search the wiki site (wiki.gromacs.org)

If you cannot resolve your problem with the above, at least give your email an 
appropriate subject line so it does not get shifted to the trash folder of an 
otherwise helpful individual who is not alerted to the question.  Usually 
subjects like "help," "error," of "I don't know what to do" get ignored because 
the answer can be solved by doing #1 or #2 above.


That said, I'll give you a hint: search the wiki, the answer is there.

-Justin



sincerely yours,
Wang Qian




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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] help

[qwang]

Hi,
I am trying to simulate a protein with a DPC micelle. Part of pdb files is:

CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1   1
ATOM  1  N   DPC M   1 -16.481  21.283  -0.739  1.00  0.00  MICE
ATOM  2  C14 DPC M   1 -15.620  20.082  -1.136  1.00  0.00  MICE
ATOM  3  C15 DPC M   1 -17.727  20.772  -0.234  1.00  0.00  MICE
ATOM  4  C16 DPC M   1 -15.792  22.061   0.317  1.00  0.00  MICE
ATOM  5  C17 DPC M   1 -16.780  22.230  -1.919  1.00  0.00  MICE
ATOM  6 H141 DPC M   1 -14.613  20.409  -1.348  1.00  0.00  MICE
ATOM  7 H142 DPC M   1 -16.000  19.717  -2.079  1.00  0.00  MICE
ATOM  8 H151 DPC M   1 -18.375  21.592   0.038  1.00  0.00  MICE
ATOM  9 H152 DPC M   1 -17.513  20.198   0.656  1.00  0.00  MICE

But when I use the command pdb2gmx, it is said "Residue 'DPC' not found in 
residue topology database". How can I deal with it? Thank you.

sincerely yours,
Wang Qian

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[gmx-users] cvs version and position restraints...

[Andrea Vaiana]

Hi everyone,

I have a small DNA duplex in a dodecahedron box. Amber forcefield. Spce 
water. I have position restraints defined for the whole duplex in my 
topology. I'm running exactly the same input script on 2, 4 and on 12 
cpus. The one with 12 produces a trajectory in which it is quite clear 
that the restraints are working: the stronger the restraints on a given 
set of atoms, the less these atoms move   away from the equilibrium 
position during the simulation. With 4 and 2 cpus, it is af if no 
restraints are used (the whole system tumbles and moves around the box), 
although I do see energy terms for the restraints in the log file...

I'm using the CVS version (downloaded June 4th).
I'm not sure but I think I remember someone having a similar problem on 
version 3.2 but I don't remember how/if it was solved. I couldn't find 
anything on the mailing lists.

Any clue about what's going on?

Thanks,
Andrea


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[gmx-users] Using user-tables for simulations in vacuum

[sapna sarupria]

Hello users,

I am trying to do a simulation of a polymer chain (which is simply a bead of
unified methane molecules) in vacuum using user-defined tables. The
interactions are Weeks-Chandler-Andersen instead of Lennard-Jones. However,
when I run the simulations, mdrun gives me a segmentation fault. When I run
simulations for the exact same configurations without the tables (and
therefore using VdW) the simulations run fine. In addition, the starting
configurations were obtained after 3ns simulations of the polymer in water.

So I was wondering if there is any issue with using user-defined tables with
simulations in vacuum. If not do you have any idea what could be going
wrong.
Some details of the mdp file:
1. pbc is turned off.
2. there is no pressure coupling.
3. center of mass removal is set to angular.
4. temperature is 298 K and berendsen thermostat is used.
5. energy groups and table are defined (correctly).
6. the cut-offs are set to 1.0nm (box size is larger than 4 nm).
7. no constraints are being used.

Thank you

Regards
Sapna
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[gmx-users] Simulation of silicon oxide surfaces

[Michael Hirtz]

Hello,

I want to set up a silicon oxide surface with varying -OH surface group for my
simulation. Does anybody know a tool that could do that or maybe even has a
topology I could start on and alter manually?

Thanks for any sugesstions,
Michael
-- 
http://www.defux.de
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Re: [gmx-users] Microcanonical MD with PBC

[David van der Spoel]

Lee-Ping Wang wrote:

Hi everyone,

I've been trying to get a microcanonical (energy conserving, NVE) MD run
with periodic boundary conditions.  I'm using the provided box of 216
water molecules and the SPC force field (flexible).  When I turn PBC
off, the energy RMSD is <0.01kJ/mol with a 0.1fs time step (energy is
conserved).  When PBC is turned on, the energy RMSD is much greater at
~50kJ/mol.  Even when I turn off the atomic charges, the energy RMSD is
still the same, so I am suspecting that at least the VdW potential
switching methods is at fault.



Did you try shifting instead of switching? See also JCTC 2 pp. 1-11 
(2006) for a comparison of (some of the) different shift/switch 
functions in different packages, including some never-before published 
trade secrets :).



Anyone able to help?

Here are the relevant parameters in the mdp file...

nstlist = 1
ns_type = grid
rlist   = 0.9
coulombtype = pme
vdwtype = switch
rcoulomb= 0.9
rvdw= 0.8
rvdw_switch = 0.5
constraints = none
pbc = xyz
tcoupl  = no
gen_vel  = yes
gen_temp = 300
gen_seed = 173529

Thanks a lot,
Lee-Ping

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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Calculating electric field vector at snapshots

[David van der Spoel]

Aaron Fafarman wrote:

Thank you for considering my proposed scheme for calculating the
electric field vector at a single site at every snapshot of an MD
trajectory. As discussed previously on this list, I have attempted to
use a virtual site with no mass and with an infinitesimal charge,
constructed from two atoms in the region of interest, and printing the
output of the force on the virtual site at every step.  The problem I
have run into is that the force on the virtual site is zero at every
step (see gmxdump below ) . I think this is because mdrun has already
redistributed the forces from the virtual site to the constructing
particles. Is there a way (a small code modification perhaps) that I
could capture the information of the force on the virtual sites before
it's been redistributed?


excerpt from gmxdump of trajectory from mdrun with integrator = md;
atom 1796 is the virtual site
.
  f[ 1795]={ 8.67412e+02, -1.41267e+02,  2.31425e+02}
  f[ 1796]={ 0.0e+00,  0.0e+00,  0.0e+00}
  f[ 1797]={-3.19446e+02, -1.38371e+03, -8.82301e+02}
.


Just in case there's some other explanation for the zero forces, I've
also included excerpts of the output of the gmxdump of the .tpr file
below:

atom[  1796]={type=  9, typeB=  9, ptype=   VSite, m= 0.0e+00, q=
1.0e-04, mB= 0.0e+00, qB= 1.0e-04, resnr=  119} grpnrs=[ 0
0 0 0 0 0 0 0 0 0 ]}

Virtual site 2:
nr: 4
multinr[division over processors]: 4
iatoms:
   0 type=364 (VSITE2) 1796 210 211


Thanks in advance for your help.

-Aaron



Message: 5
Date: Thu, 05 Jun 2008 08:53:32 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Calculating electric field vector at
   snapshots
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Aaron Fafarman wrote:

Dear GMX community,

I would like to calculate the electric field vector at a point in
space in a protein at many snapshots during an MD trajectory. I
haven't found a built-in function for doing this in Gromacs--is there
one? If not, would people please comment on this proposal for how to
do this:

1. Include a virtual site referenced to the two atoms (constructing
particles) that define the point in space I would like to interrogate.
Give it only a very small charge, so small that the force from the
virtual site to the constructing particles is negligible.

2. Have the calculation output the force on the virtual site at a
determined interval by setting nstfout in the.mdp file

3. Divide the force by the small charge, and hence get the field

It seems like this should work as long as the force on virtual sites
is reported in the output of forces from nstfout, and as long as using
such a small charge on the virtual site will not run into rounding
errors. Also I'm presuming that the coulomb interaction is not
calculated between the constructing atoms and the virtual site--is
that correct? Any thoughts?


I think it will work. Just try it.


It could be that the force is set to zero after distributing it. Check 
the src/mdlib/vsite.c code. You could modify this code, such that it 
does not reset the forces. Be careful that this does not generate other 
problems (you can check by comparing runs with and without this feature 
using gmxcheck -e -e2 -tol 0).


The proper way to do this would be to recompute the non-bonded forces 
(short range only) with LJ parameters set to zero. The contribution to 
potential and field from PME can be extracted without too much trouble.







Thanks,

-Aaron
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