Dear Justin,
>> Parameterization is a hard road that takes a lot of time
I agree and thanks for reply
On Thu, Jul 25, 2013 at 3:47 PM, Justin Lemkul wrote:
>
>
> On 7/25/13 8:41 AM, gromacs query wrote:
>
>> Dear Justin,
>>
>> Thanks this paper
wrote:
>
>
> On 7/25/13 8:25 AM, gromacs query wrote:
>
>> Dear All,
>>
>> I am working on some molecule and I have defined atom types with OPLSaa
>> and
>> all atom types really exist in oplsaa and well chosen so no approximation
>> in choosing atom
Dear All,
I am working on some molecule and I have defined atom types with OPLSaa and
all atom types really exist in oplsaa and well chosen so no approximation
in choosing atom types. During grompp, I found there are dihedral param
missing. e.g.
N CT CT NT
N CT CT N3
Is there any 'good' way of fi
01 PM, Justin Lemkul wrote:
>
>
> On 7/17/13 1:33 PM, gromacs query wrote:
>
>> Dear Justin,
>>
>> Thanks for reply and explanation, and..:
>>
>> you've got an amide flanked by two methylene groups as the repeat unit
>>>> All the amino acids
tin Lemkul wrote:
>
>
> On 7/17/13 11:39 AM, gromacs query wrote:
>
>> Dear Justin,
>>
>> 1) I can understand the improper for stereocenters (chiral) easily but
>> with
>>
>
> OPLS doesn't use impropers for chiral centers.
>
>
> bonds I am
:
>
>
> On 7/17/13 10:37 AM, gromacs query wrote:
>
>> Dear All,
>>
>> I have some polymer having peptide bond and want to use OPLSaa. I was
>> following Justin's example for building polymers
>> http://lists.gromacs.org/**pipermail/gmx-users/2009-**March/040
Dear All,
I have some polymer having peptide bond and want to use OPLSaa. I was
following Justin's example for building polymers
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html
I have few queries:
1) do I need to define improper for peptide in .rtp file to keep it planar?
2)
blem a while ago. The simplest way to deal with it is just to add a
> letter at the end of your atomtypes.
>
>
>
>
> 2013/6/20 Mark Abraham
>
> > Probably
> >
> > Mark
> > On Jun 20, 2013 11:42 AM, "gromacs query"
> wrote:
> >
> >
Dear All,
I have a complex A-B (not covalent bonded)
I want to use oplsaa.ff atom types original for A and all are in .top files
in which some parameters are changed and I have another directory with
modified just atomtype names oplsaa.ff files (for B) that is ffbonded.itp,
ffnopnbonded.itp, atom
gt; used is listed and the sets of parameters are also listed and the
> cross-reference is made. But it is not really intended for human digestion.
> You haven't stated your purpose for the information, so it's hard to be
> helpful.
>
> Mark
>
>
> On Tue, Jun 18, 2013
3658
>
> > -Ursprüngliche Nachricht-
> > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > boun...@gromacs.org] Im Auftrag von gromacs query
> > Gesendet: Dienstag, 18. Juni 2013 10:42
> > An: Discussion list for GROMACS users
> > Betreff: Re: [gmx-u
xtract params from oplsaa for all these. Or do I need to map
atom types for these atom numbers then only I can extract or is there any
inbuilt Gromacs module in this regard
regards,
On Tue, Jun 18, 2013 at 11:32 AM, Mark Abraham wrote:
> Grep?
> On Jun 18, 2013 10:23 AM, "grom
Dear All,
Is there any way to print parameters used for system (just for the
atomtypes present in system). I have all necessary files (top, tpr, gro and
oplsa.ff)
regards,
Jiom
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search
Dear Justin,
Thanks a lot. I used this and it works fine:
editconf -f final.pdb -o final.gro -c -d 0.0
regards,
Jiomm
On Sat, Jun 15, 2013 at 3:09 AM, Justin Lemkul wrote:
>
>
> On 6/14/13 8:08 PM, gromacs query wrote:
>
>> Dear Justin,
>>
>>
possible way? If I just use
system size dimension (X, Y Z) and do mimization it break my system in
parts!
How to choose optimum box vector in such case?
regards,
On Sat, Jun 15, 2013 at 2:49 AM, Justin Lemkul wrote:
>
>
> On 6/14/13 7:37 PM, gromacs query wrote:
>
>> Dear Ju
, 2013 at 1:37 AM, Justin Lemkul wrote:
>
>
> On 6/14/13 4:58 PM, gromacs query wrote:
>
>> Dear All,
>>
>> I have two different membrane systems (membrane with waters only) already
>> with me. So I dont need to add solvent molecules.
>>
>> So to sta
Dear All,
I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.
So to start with simulation I need box size (last line in gro file). I used
following command (for both cases):
editconf -f del.pdb -o del.gro -c -bt cubic
Firs
Dear All,
Please any suggestion?
regards,
On Mon, Jun 3, 2013 at 4:53 PM, gromacs query wrote:
> Dear All,
>
> (Sorry for long mail!)
>
> (Thanks Thomas Schlesier for clarifying previous umbrella queries)
>
> I wish to run umbrella samplings using restart file of p
Dear All,
(Sorry for long mail!)
(Thanks Thomas Schlesier for clarifying previous umbrella queries)
I wish to run umbrella samplings using restart file of previous window.
e.g. initial distance between A (reference) and B (pulled group) is 1 nm
(10 Angs) then I intend to run 10 windows after eac
romcacs! for such case
regards,
On Fri, May 31, 2013 at 10:03 PM, gromacs query wrote:
> Dear Thomas,
>
> Thanks a lot again for great reply. Please clarify this also,
>
> >> If one uses only 'Y N N' B would only move along the x-axis due to the
> pull, but could
Dear Thomas,
Thanks a lot again for great reply. Please clarify this also,
>> If one uses only 'Y N N' B would only move along the x-axis due to the
pull, but could move freely in the yz-plane
>>You never want to use the pull-code and 'pull_dim = N N N'
>>This would mean that there is no force ac
Dear Thomas,
Thanks a lot for your time and nice explanation. I was not able to get
specially the pull_start flag but now its quite clear.
I feel sorry, that should be pull_dim = N N N in my case. Also I will be
much thankful if you please can help me to make understand following:
1)
>> If you d
Dear Lloyd,
I have read that but my system is different
regards,
On Thu, May 30, 2013 at 8:28 PM, lloyd riggs wrote:
> Dear Jiom,
>
> Look at justines tutorial, there's example pull .mdp.
>
> Stephan Watkins
>
> *Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 U
Dear All,
I want to do Umbrella sampling between two different polymers (A and B)
interacting with each other with starting configuration separated by some
distance and I am trying to bring them closer.
I have some queries regarding pull inputs: (this is for to run a umbrella
sampling at some dis
Dear All,
I have a system with two solutes (A and B) with water and ions. For
pressure coupling in index file I defined two groups: Solute and Solvent,
where solute consists of A+B and solvent consists of water+ions
Due to some reasons I need to apply position restraints on Solute A only
for few
>> Gromacs do not use residue number or atom number,
OK! Thanks Nuno and Mark
regards,
On Tue, May 14, 2013 at 7:14 PM, Mark Abraham wrote:
> Try selecting residue 0 with editconf and see for yourself :-)
> On May 14, 2013 4:41 PM, "gromacs query" wrote:
>
>
t; Nuno Azoia
>
>
> On Tue, May 14, 2013 at 3:08 PM, gromacs query >wrote:
>
> > Dear All,
> >
> > I have a huge system and residue number goes beyond 9. So when I
> added
> > waters then residue number goes till 9SOL then again it starts from
>
Dear All,
I have a huge system and residue number goes beyond 9. So when I added
waters then residue number goes till 9SOL then again it starts from
0SOL. I tried genconf -renumber option but it does not help.
Though it can be done with small scripting, just want to know if it can be
done
, 2013 at 1:07 PM, Justin Lemkul wrote:
>
>
> On 5/6/13 4:21 AM, gromacs query wrote:
>
>> Dear All,
>>
>> I want to calculate water and ions density around polymer. After MD I see
>> my polymer goes near the edges of box and rather some part is out of box.
>
Sorry forgot to add:::
by doing this I can see my polymer near the center of box
On Mon, May 6, 2013 at 11:21 AM, gromacs query wrote:
> Dear All,
>
> I want to calculate water and ions density around polymer. After MD I see
> my polymer goes near the edges of box and rather some
Dear All,
I want to calculate water and ions density around polymer. After MD I see
my polymer goes near the edges of box and rather some part is out of box.
So in order to calculate water and ion density I think polymer should be
near the center of box (please correct me if wrong)
So by doing th
,
On Thu, May 2, 2013 at 12:50 AM, Mark Abraham wrote:
> On Wed, May 1, 2013 at 4:20 PM, gromacs query >wrote:
>
> > Dear All,
> >
> > I am using Charmm gui built membrane (120 x 2). But during minimization I
> > was getting error.
> >
> > Potenti
Dear All,
I am using Charmm gui built membrane (120 x 2). But during minimization I
was getting error.
Potential Energy = 4.6809051e+19
Maximum force =inf on atom 4281
Norm of force =inf
(inf means? means infinite/NAN)
I removed the full lipid residue having
Dear All,
I have a pdb file in which has only heavy atoms (means all atoms except
hydrogen) and a corresponding itp file with all atoms (including
hydrogens). The heavy atoms in pdb file are in sequence order as in itp
file.
e.g.
itp pdb (no Hydrogens)
*
C1 C1
H1 C2
Thanks a lot Dr. Justin
On Wed, Mar 6, 2013 at 2:52 PM, Justin Lemkul wrote:
>
>
> On 3/6/13 7:35 AM, gromacs query wrote:
>
>> Dear All,
>>
>> How md engine in GROMACS (mdrun) detects which energy function to be used
>> as it varies for differen
wrote:
> Hi,
>
> Then the problem lies in automating what molecules are to be removed,
> right? Try g_select or look into trjorder.
>
> Erik
>
>
> On Mar 1, 2013, at 2:45 PM, gromacs query wrote:
>
> Aha! thanks Erik (and Justin),
>>
>> I really feel sor
criteria based on X Y Z
coordinates (some space fixed and outlier waters are to be removed)
regards,
On Fri, Mar 1, 2013 at 3:09 PM, Erik Marklund wrote:
>
> On Mar 1, 2013, at 2:08 PM, Erik Marklund wrote:
>
>
>> On Mar 1, 2013, at 1:58 PM, gromacs query wrote:
>>
>>
s really simple. You can easily script your way to a new
> index group as long as the selection of atoms can be automated.
> Furthermore, the gro format is also simple, so you can filter out the
> unwanted residues there instead of using an index file.
>
> Erik
>
>
> On Mar 1, 2013
Dear All,
I know the residue numbers of SOL molecules (which are more than thousands)
which I want to remove them from a gro file. I searched that make_ndx can
be used make a index file to define residues. But It is a prompt based tool
and its difficult to type manually thousands of residue number
Dear Justin,
thanks its working, sorry it was my mistake I used wrongly /usr/local/bin,
so export LD_LIBRARY_PATH=/usr/local/lib is working fine now.
regards,
On Sun, Nov 4, 2012 at 11:02 PM, Justin Lemkul wrote:
>
>
> On 11/4/12 12:23 PM, gromacs query wrote:
>
>> Dear Jus
=$PATH:$LD_LIBRARY_PATH (tried by including and not including
this)
source /usr/local/gromacs/bin/GMXRC
thanks,
On Sun, Nov 4, 2012 at 10:38 PM, Justin Lemkul wrote:
>
>
> On 11/4/12 12:01 PM, gromacs query wrote:
>
>> Dear All,
>>
>> I have installed gromacs-4.5.5
Dear All,
I have installed gromacs-4.5.5 on CENTOS 64 bit. I have tried following
options and I was successful to install by all of following methods but
every time I am getting this error when I use any command e.g. mdrun,
g_analyze
error while loading shared libraries: libfftw3f.so.3: cannot ope
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