own is a hammer, every problem begins to resemble a
nail.
** **
*From:* gmx-users-boun...@gromacs.org [mailto:
gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed
*Sent:* Friday, 16 September 2011 12:55 AM
*To:* jalem...@vt.edu; Discussion list for GROMACS users
*Subject:* Re: [gmx
and please
comment on the attached plot if you have any ideas. Thank you. :)
Moeed
On Sat, Sep 10, 2011 at 10:00 AM, Moeed lecie...@googlemail.com wrote:
Thank you for your input. I am going to run for another 15 ns to see if the
little jumps vanish.
Best,
On Fri, Sep 9, 2011 at 9:16 PM
Thank you for your input. I am going to run for another 15 ns to see if the
little jumps vanish.
Best,
On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Sat, Sep 10, 2011 at 3:35 AM, Moeed lecie...@googlemail.com mailto:
lecielll@googlemail.**com
Dear users,
I have created radial distribution function plot for Carbon atoms in a
system containing polymer chains. I see some little jumps between first and
second peak.
I need your help to comment on how this behavior can be justified (or if the
plot is wrong).
g_rdf -f *.trr -s *.tpr -o
Thank you Justin for your reply. Simulation is 5 ns long ( before this a 500
ps NVT was done as equilibration) and total energy has been equilibrated
after around 3 ns.
-b is set to 4000 that is the last 1 ns has been used for rdf.
Best,
moeed
On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul
On Fri, Sep 9, 2011 at 4:18 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long ( before this a
500 ps NVT was done as equilibration) and total energy has been equilibrated
after around 3 ns.
-b is set to 4000
On 14 April 2011 02:11, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/04/2011 3:40 PM, Moeed wrote:
On 13 April 2011 18:45, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/04/2011 10:22 AM, Moeed wrote:
Hello,
I have run 2 ns simulations on a hydrocarbon system (initial density
So Sorry I did not mean to be rough :) . Thanks for your comments...:)
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to further compression but
causes the box expand to a much bigger size!
How can this be justified?
Thanks for your suggestions,
moeed
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Hello,
I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
SI and box size is 15 nm), one with version 4.0.7 and the other trial using
4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is
giving density of above 600SI (4.0.7) and the other density of
On 13 April 2011 17:14, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/04/2011 4:36 AM, Moeed wrote:
Hello everyone,
I have encountered a strange behavior while compressing a pure system.
I am applying 100 bar pressure with PME and it turned out that this
pressure leads to density
On 13 April 2011 18:45, Mark Abraham mark.abra...@anu.edu.au wrote:
On 14/04/2011 10:22 AM, Moeed wrote:
Hello,
I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2
SI and box size is 15 nm), one with version 4.0.7 and the other trial using
4.5.3. Both runs
-deffnm when you run your mdrun to get all the out put files
by
default.
The -deffnm flag controls the names of the files, not which ones are
written.
-Justin
Cheers,
*From:* gmx-users-boun...@gromacs.org [mailto:
gmx-users-boun...@gromacs.org] *On Behalf Of *Moeed
*Sent:* Thursday
Hello,
I have a little problem with FE output file. Below is the settings and also
I am including -dgdl in the command I issue but no dgdl (or dhdl) file
generates. I dont figure where the problem lies ! (version 4.5.3).
free_energy = yes
init_lambda = 0
delta_lambda
Hi Justin,
I was looking all the time for a file with dgdl extension throughout the
directory. IIRC in previous versions -dgdl would generate such extension. I
found now .xvg file which has dhdl data. (if I am right dgdl is the very
dhdl in 4.5.3!)
I have a little problem with FE output
Hello,
I am compressing a single extended PE chain (16 nm in length) in a box of
20nm in vacuo to get a more realistic shape of the polymer. Although system
is small (only 362 atoms), whatever -np # I choose simulation runs very
slowly. Is that because of the presence of voids? Is there a way to
the time that gives the desired density and extract
that frame ( with command above) followed by NVT to equilibrate and use that
as prodcution run?
Please help me with this.
Thanks a lot,
Moeed
===
step 449800, will finish Tue Mar 15 11:23:55 2011
step
On 20 March 2011 15:23, Justin A. Lemkul jalem...@vt.edu wrote:
Moeed wrote:
Dear experts,
I am trying to build up a polymer in hexane system by increasing the
density and use this for FE calculation. After PR step, my NVT and NPT
trailes failed. Initially I used to get LINCS and 1-4
( with command above) followed by NVT to equilibrate and
use that as prodcution run?
Please help me with this.
Thanks a lot,
Moeed
===
step 449800, will finish Tue Mar 15 11:23:55 2011
step 449900, will finish Tue Mar 15 11:23:55 2011
[node5:09563] *** Process
dh_hist_size = 0
dh_hist_spacing = 0.1
Please give me some advice..
Thanks
-Justin
Moeed
===
step 449800, will finish Tue Mar 15 11:23:55 2011
step 449900, will finish Tue Mar 15 11:23:55 2011
[node5:09563] *** Process received signal
fit in the box.
Moeed
===
step 449800, will finish Tue Mar 15 11:23:55 2011
step 449900, will finish Tue Mar 15 11:23:55 2011
[node5:09563] *** Process received signal ***
[node5:09563] Signal: Segmentation fault (11)
[node5:09563] Signal code: Address
dh_hist_size = 0
dh_hist_spacing = 0.1
Moeed wrote:
Hello Justin,
I just scanned through the manual and also looked into the list to learn
about the significance of reciprocal part to realize your statement. I did
not find much about the fact that how I can judge
Hi,
Please don't #include ions.itp in your topology file if not needed.
moeed
On 10 March 2011 13:22, tao wei twei2...@gmail.com wrote:
Hi
I saw your post on Gromacs forum about the
Fatal error:
Atomtype CU2+ not found
http://lists.gromacs.org/pipermail/gmx-users/2010-September/053804
Hello,
If you need to keep ions.top then see the below link:
http://lists.gromacs.org/pipermail/gmx-users/2010-September/054487.html
moeed
On 10 March 2011 14:53, tao wei twei2...@gmail.com wrote:
Dear Moeed,
Thanks a lot for your quick response!
That is problem. I do need to include
mixture
properties?
I appreciate your help.
Best,
moeed
Regards,
Thomas
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx
take care
of.
Thanks,
Best,
Moeed
step 164300, remaining runtime: 241 s
step 164400, remaining runtime: 240 s
step 164500, remaining runtime: 240 s
step 164600, remaining runtime: 239 s
Warning: 1-4 interaction between 260 and 267 at distance
below.
-Justin
Thanks,
Best,
Moeed
step 164300, remaining runtime: 241 s step 164400, remaining
runtime: 240 s step 164500, remaining runtime: 240 s
step 164600, remaining runtime: 239 s Warning: 1-4 interaction
Hello,
I am attempting to increase the density using NPT. As I increase the
pressure to compress the system after some steps simulation crashes. I
thought maybe its becasue I am compressing too fast but even when I take a
stepwise approach to compress gradually the same error comes up. The
would you deal
with this? What value would you pick?
Thank you,
moeed
fourierspacing = 0.3
You're setting yourself up for inaccurate PME calculations with this. Use
0.1 - 0.12 unless you've got some compelling reason to decrease your
accuracy.
-Justin
Thank you for your helpful comments. I am totally convinced that I was not
using proper force field.
Best,
moeed
On 28 February 2011 18:12, Justin A. Lemkul jalem...@vt.edu wrote:
Moeed wrote:
Dear Justin,
Thank you for your message. My objective is to calculate interaction
energies
interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web:
http
=458507_coverDate=11%2F30%2F2000_rdoc=1_fmt=high_orig=search_origin=search_sort=d_docanchor=view=c_searchStrId=1650178009_rerunOrigin=google_acct=C22002_version=1_urlVersion=0_userid=458507md5=bf0b74cfc76e0dafbadf06396fb63745searchtype=a
Please let me know your comments
Thanks
Moeed
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with
DD (nm), 0 is determine from initial coordinates
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
***
Thanks,
Moeed
BTW: About mdp setting for electrostatics, I have set zero charges to all
atoms so there is no electrostatics term
===
Please help me what wrong is...
Thanks
moeed
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Thanks
Moeed
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Dear experts,
I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom type
CU+2. I am not using such atom type at all! Could you please help me what
wrong is. Thanks.
My system contains only C and H atoms!.
Hello Justin,
1- Actually since I was focusing on rdf for C-C I didnt explain my
understanding from that post well. Anyway, I have only C and H in the system
and no protein. You mean I have to make separate groups of C and H for all
polymer chains by hand? I trying to find a more smart way of
Dear experts,
I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom type
CU+2. I am not using such atom type at all! Could you please help me what
wrong is. Thanks.
grompp -f *.mdp -c *.gro -p *.top -o out
Hello,
1- In the manual I see rdf plot for Oxygen-Oxygen of SPC-water. I think
this shows the average O-O density between all water molecules. I read a
post saying that rdf is calculating C_C distances for each C on chain 1 for
instance and all other C on the chain and other chains..
:
@TYPE xy
0.000 nan
0.100 nan
0.200 nan
0.300 nan
0.400 nan
0.500 nan
0.600 nan
0.700 nan
0.800 nan
0.900 nan
. .
Thanks,
moeed
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Hello Justin,
I have read help of the command I am using several times. My understanding
is that g_polystat calculates Rg of 8 chains and takes the average if no
specific index groups are selected. Below are the groups I have created for
8 chains.
g_polystat -f *.trr -s *.tpr -o
gives Rg for nmol number of molecules to be analyzed. What does Rg refer to
if command is used without nmol?
I dont realize why results are different and why they demonstrate.
Thanks for your comments
moeed
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Hi,
We are installing the newest version of Gromacs - 4.5 on our cluster
(running CentOS) for parallel purposes. We are also using Openmpi version
1.4. However upon installing Gromacs using the command:
./configure --enable-mpi
we ran into this problem below:
* Seems you are compiling with
of molecules?
I know manual can not be wrong but from what I see it makes more sense if
unit is energy/system!
Thanks,
2010/8/27 Vitaly Chaban vvcha...@gmail.com
Dear Moeed:
1. Please note, this is Justin here who likes long descriptions but I like
those which are as short as possible
and if there are
10*Na, g_energy divides total energy by 10. Please enlightem me on this
issue. Many thanks
Moeed
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tried both
semiisotropic and isotropic options but the same behaviour has been
observed.
I appreciate any help and comment...
Moeed :)
**
Energy Average RMSD Fluct. Drift
Tot-Drift
Hello Justin,
Please let me explain my naive procedure to make index file so that you can
make comment. I have created the top file for a single solvent molecule.
Then removed [system] , [molecule] directives as well as #ffgmx.itp. The
[molecule type] is named 'solvent''. I got a sample itp file
parameters (which are
calculated for low pressure) at higher pressures?
Moeed :)
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Hello,
My efforts for compressing a polymer chain all failed. Even when I am
compresing very slowly with tau-p=10 and ref_p of 1 bar simulation crashes
when box size is close to chain size.. I tried different pressures of 1 10
30 and tau_p of 1 2 5 10 and cobination of these...Has anyone idea on
Dear gmx users,
I am trying to compress a single polymer chain. grompp is giving the error
below:
Program mdrun, VERSION 4.0.7
Source code file: ns.c, line: 2299
Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller
obtained a
total energy of 2000 Kj/mol. I am curious why results are not the same. Are
you sure you did the simulation with 8 molecules and not with a single
chain?
Sorry to have bothered you..
Moeed
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for
compressing system for all systems?
2- You said I dont need NVT at all. But if I want to study the system I get
from NPT giving the density I want, can I not do NVT for a fixed system size
and calcualte energies or other quantities I am after?
Thanks for your attention
Moeed
Energy
Dear Dr. Chaban,
Thank you for your attention. Actually with the revised mdp file you sent me
and the initial configuration of my 8PE system, I tried to compress the
system. The simulation tales very long and produces nothing. grompp is
giving me:
processing topology...
Analysing residue names:
using shift functions for vdw and electro reduces
simulation time significantly as compared to cutoff! Why is that happening?
Thanks
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Graduate Student (Materials Modeling Research Group)
McGill University- Department of Chemical Engineering
Montreal, Quebec H3A 2B2, Canada
Web
Dear experts,
I am trying to build up a polymer system. To do so I took a chain with 60
repeating units (ethylene) and compressed the system to attain the desired
box volume (density). I took the following approach since after one week
work on this problem I believe that is the only way of
Hello,
Thanks for your reply. As for the simulation box, I did not change anything
and I am still saying that I am having a cubic box of size 30nm. When I view
the molecule in ngmx I see the cubic box.. no problem with that. What I was
referring to was the option on menu bar where one can select
Hello,
I followed the hints. I did several NPT runs and I found out pressure above
100 eg 120 bar gives final boxsize close to volume of box I want. But I dont
know why pressure given by g_energy is totally different.
1- I looked at values in xvg file and I notoced pressre starts froma very
low
Hello,
Thank you for suggestions. Yes simulation crashes. I am not able see the
whole run (1000ps). For all pressures I tired the final simulation box is
2.2*2.2*2.2 nm but simulation crashes before 1000ps. The longest simulation
is for 120 bar (727ps). and I think that is why I am not getting
Hello,
Sorry I did not paste the error message part properly. Initially I am trying
to study PE in vacuum (current box size 30*30*30 nm) and then I will solvate
the PE with Hexane.
NOTE 1 [file md-July11-NPTcompression.mdp, line unknown]:
The Berendsen thermostat does not generate the correct
Hello everyone,
I am trying to energy minimize a system of 8 polyethylene molecules with 60
units. In literature density of PE is reported 0.9 gr/cm3. Based on this I
need to have each single chain in 3.3 nm^3. If I put this chain in a box of
15*0.5*0.5 =3.75 nm^3 I am close to the density I
actual NPT and NVT simulations with this packed
system. Can I not do NVT with this density?
Thanks,
Moeed
In PE60-3.75nm3.gro enlarge the box size. Then use NPT simulation to
compress the MD box.
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Dear Justin,
Thanks so much for your help. The structure looks almost fine now.
1-I am getting bond distance of 1.52 or 1.53 and angles of 112.2 / 112.0
with -d 0.0584/ 0.0581. Actually when I open up the same structure file in
VMD at different times I see even a little difference in bond
*I read thorough the manual on index groups and creating index file. This is
the command I tried:
make_ndx -f index.gro -o index.ndx
*
with index.gro you proposed:
[ special ]
1 3
[ all ]
1 2 3 4
error I get:
Reading structure file
Hello Justin,
I spent a full day to find a proper value for -d but it seems there is no
way of getting correct bond lenght and angle at the same time. With the
following commands I am getting correct bond length for the atoms connecting
two monomer units but the angle is 140. I get 110 angle
to do with PE chain.
Thanks for your attention.
Moeed
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moeed
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of repeating unit -CH2-CH2- with
PRODRG. I tried the followings...and all I am getting is the above message..
:(
H H
| |
C-C
| |
H H
H H
| |
-C-C-
| |
H H
-C-C-
Moeed
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Hello Justin,
I created structure file for a 4-carbon repeating unit as follows:
HETATM1 CAA DRG 1 14.260 -4.270 0.000 1.00
20.00 C
HETATM2 1HAA DRG 1 14.175 -3.426 0.530 1.00
20.00 H
HETATM3 2HAA DRG 1 15.050 -4.790 0.326
!
Thank you,
Moeed
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opls_140 0.0602
H22 opls_140 0.0602
[ bonds ]
C1-C2
C1H11
C1H12
C1C2
C2H21
C2H22
C2+C1
Q 2-2. Does x2top command have advantage over pdb2gmx command with regards
to atom numbering?
Many many thanks,
Best,
Moeed
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...!
Thank you for your time :)
MOeed
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a a lot of changes manually which is a nightmare for big
chains.
Thanks,
Moeed
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Hello,
I have 125 hexane molecules in a box of 0.25nm3. The desnity I calculate
from this number of molecules is approx. 71000 Kg/m3. To make sure that the
density remains constant I am doing NPT simulation. From this simulation I
see the density is 577 Kg/m3. and the volume is 30 nm3. Please
is investigating the conformations of a much longer
chain. Could you please tell me how to generate a longer chain with the
given residue types proposed in the above post.
thank you,
moeed
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Please
appreciate your help.
Thanks
Moeed
*mdrun -rerun on trajectory for nrexcl=2 in top file*
Energy Average RMSD Fluct. Drift
Tot-Drift
---
Angle 4286.19258.765
Hello Justin,
The energy values I get differ mainly for LJ and coulomb(SR) terms. I read
through chapter 4 of manual but I did not find the difference between
LJ/coulomb 1-4 and SR.
1-Where can I read about the differences of these?
2-Do you think the difference in energies as a result of
Dear experts,
I am trying to exclude all nonbonded interaction on hexane molecule.
1-For the md -rerun command I do not know how to get the input XTC file. the
program is expecting rerun.xtc
mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o
ORIGINAL-Trajectory-NOexcl.tpr* -c
approach (nrexcl in moleculetype) and let me know what wrong is..
Thank you,
moeed
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= all-bonds
constraint-algorithm= lincs
*;Energy group exclusions
eneegygrp_excl = HEX *
pbc=xyz
/*topology file:
;
;File 'Hexane-PRODRG.top' was generated
;By user: moeed (500)
;On host: moeed-desktop
;At date: Tue May 11 09:31:28 2010
Hello Justin,
Thanks for your comments. Actually, since I am interested in only
interaction energies *between* molecules I thought by excluding energies
between atoms on a single chain what I get from nonbonded interactions would
not include 1-4 interactions.
Hi,
could you guide me how one can create .ndx file format. I thought it would
be accessible in library directory like rtp ..files.
Thanks,
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Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system.
To do this how should I define my index groups. Should I include all 125
molecuels in index file? now I have only the first 20 atoms (first
Hello,
I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules (interaction energy between two hexane
molecules) I have 125 hexane molecules in my system. Please help me figure
out what the problem is.
make_ndx -f Hexane-Stack125.gro -o index.ndx
, Hexane, how many molecules i need to put in a simulation box.
3- Do I need to consider free energy of solvation for this type of
calculation?
Many thanks,
Moeed
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NO. of molecuels
in simulation box and calculate interaction energies for pairs or mol
number of molecules?
Thank you for you help :)
Moeed
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Dear experts,
I am trying to do a MD run for stack of hexane molecules. The density of
hexane (Mw 86 g/mol) is about 1 g/cm^3.
Density (g/cm3) Mw hexane (g/mol) NO.molecuels/cm3NO./nm3 1 86
1/86*6.023E23=7.0E+21 7
using genconf I generated 1000 molecules in 160 nm^3 which gives
Hello,
I intend to generate a stack of molecules with the command line:
genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro
Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 molecules
per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 molecuels.
What I get from the
Dear gmx users,
I tried to generate a stack of molecules using
*genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o
Hexane-stack.gro*
I ran the MD simulation successfully but now I want to change the number of
molecules so that I get the desired system density. To do so I played
Dear GROMACS experts,
Initially I wanted to do MD for a stack of hexane molecules. MD showed very
high repulsion potential. On the recommendation of Justin, I simplified the
problem and now I have only one Hexane molecule.
1- I dont know why I do not get the written pdb files normally generated
There are: 0PROTEIN residues
There are: 0DNA residues
Analysing Other...
This run will generate roughly 0 Mb of data
***
;
;File 'Hexane-PRODRG.top' was generated
;By user: moeed
-p Hexane-PRODRG.top -ff
oplsaa output.pdb2gmx
I do not get gro file at all and top file I get contains the following
comments only!:
;
; File 'Hexane-PRODRG.top' was generated
; By user: moeed (500)
; On host
atoms
chain #res #atoms
1 'H' 1 20
Reading residue database... (ffoplsaa)
Processing chain 1 'H' (20 atoms, 1 residues)
Moeed wrote:
Hello,
I am trying to generate gro and top file with pdb2gmx program. I have
made a copy of ffoplsaa.rtp from library to working directory
Dear Justin,
1- Unfortunately, I am having difficulty running the simple program pdb2gmx
with pdb file you sent me for Hexane.. I have in working directory pdb file
and rtp files:
Hexane-PRODRG.pdb rtp.pdb
pdb2gmx -f Hexane-PRODRG.pdb -o Hexane.gro -p Hexane.top output.pdb2gmx
output.pdb2gmx
Dear Justin,
Thank you so much for your help. Could you please help me with some simple
questions:
1- Regarding the atom types: For n-Hexane why did not you choose atom types:
opls_068 15.03500 ; CH3 (C2) N-ALKANES
opls_071 14.02700 ; CH2 (SP3) ALKANES
rather than:
opls_157 12.01100
density?)
2-2 Dies the idea of changinf cut off radius (you mentioned somewhere
inthe archive) would work?
3- How Can I view the potential energies arising form various contributions?
(electrostatics, vdw,..) to see which type is causing problem?
Thank you for your help.
Moeed wrote:
Dear
'Hexane.top' was generated
;By user: moeed (500)
;On host: moeed-desktop
;At date: Thu Apr 8 13:51:19 2010
;
;This is your include topology file
;Generated by x2top
;
; Include forcefield parameters
#include ffoplsaa.itp
[ moleculetype ]
; Namenrexcl
HEX
Dear gmx experts,
I am having problem doing MD run for a hydrocarbon system. The system
contains a stack of Hexane molecules using editconf.
The distance between molecuels in the box is more than 30 A. I am wondering
why I get large forces (system is blowing up) with this distance!. (LINCS
Dear Justin,
1- Could you please check if I have grouped atoms properly? Lastly, I could
generate the tpr file for PR step. Since I am getting segmentation fault in
the next step I though maybe there is sth wring with charge groups..
However, I have a funda,mental question. I am to compute
I would be most thankful if you could help me warning 1, note 1 and thr
fatal error. I I read about -n option but I dont know where in command line
i have to include it. Thank you.
grompp -f pr -c Hexane_b4pr.gro -r Hexane_b4pr.gro -p
HexaneModified-Residuename.top -o Hexane_pr output.grompp_pr
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