Hi,
I have read a couple of posts on related topics but I am still not
sure how to proceed and would be grateful to get some help.
I want to run implicit solvent simulations of a protein+water
(implicit) system in the canonical ensemble using charmm27+cmap
forcefield. I am trying to use the param
8 PM, Mark Abraham wrote:
> On 25/10/2011 9:54 AM, Sai Pooja wrote:
>>
>> Hi all,
>>
>> I am using GROMACS with the plugin PLUMED in double precision. The
>> speed has gone down by a huge margin and I was wondering if there is
>> something in 1) compilation 2) md
Hi all,
I am using GROMACS with the plugin PLUMED in double precision. The
speed has gone down by a huge margin and I was wondering if there is
something in 1) compilation 2) md parameters that could be
contributing to this?
md parameters:
title= NVT simulation (constant num
Hi,
It is not clear what are the units of SAS from g_SAS. The output gives
the units - xaxis label "Time (ps)"
@yaxis label "Area (nm\S2\N)".
I would really appreciate it if someone could elaborate on (nm/S2/N).
Thanks and regards,
Pooja
--
Quaerendo Invenietis-Seek and you shall disco
But is the effect of varying ld_seed.. can that make different
trajectories stochastic?
On Wed, Sep 21, 2011 at 7:40 PM, Mark Abraham wrote:
> On 22/09/2011 6:21 AM, Sai Pooja wrote:
>>
>> Hi,
>>
>> The sd integrator is described in the manual as follows:
>
Hi,
The sd integrator is described in the manual as follows:
sd
An accurate leap-frog stochastic dynamics integrator. Four Gaussian
random number are required per integration step per degree of freedom.
With constraints, coordinates needs to be constrained twice per
integration step. Depending on
Hi,
I am running essential dynamics for a protein in water system (charmm-nocmap
and tip3p). I use the first 25 eigenvectors and targeted ED. It stops after
630ps when settle and lincs start giving warnings.
Step 315573, time 631.146 (ps) LINCS WARNING
relative constraint deviation after LINCS:
reversibility.
Also, I dont think I can apply it a fixed vector (as in specify the vector
from one atom to the other) because I dont think the path will be a straight
line.
Pooja
On Fri, Apr 1, 2011 at 8:02 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> The pull tutorial us
Hi
Precision mismatch for state entry nosehoover-xi, code precision is double,
file precision is float
I am trying to extend an mdrun from a restart file. I get the error pasted
above. The restart file was generated on a different cluster and I am now
extending these simulations. Can this be reso
eate a
> merged [moleculetype] to apply distance restraints. If you're just trying
> to use a harmonic potential to define some sampling distance (for US), then
> distance restraints are not necessary, just apply the pull code.
>
> -Justin
>
> Sai Pooja wrote:
>
>>
Also, the chains do not diffuse apart in time since they are position
restrained(some parts of each chain are ...)
On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja wrote:
> Hi,
>
> I have 5 chains in my Protein. I want to apply distance restraints for
> doing Umbrella Sampling for 2 atoms
Hi,
I have 5 chains in my Protein. I want to apply distance restraints for doing
Umbrella Sampling for 2 atoms on different chains. Is there a way to do this
since the two chains have separater itp files.
Pooja
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On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham wrote:
> On 1/04/2011 1:30 PM, Sai Pooja wrote:
>
>> Hi,
>> This is regarding the energygroups that one can use in the mdp file for
>> tracking energy. Are these the groups defined in the index file?
>>
>
> Y
Hi,
This is regarding the energygroups that one can use in the mdp file for
tracking energy. Are these the groups defined in the index file?
I want to know if I can define a subset of atoms in the index file and track
its energy.
Pooja
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--
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It is working. The error was clerical. Thank you for your time.
On Tue, Mar 29, 2011 at 10:52 AM, Sai Pooja wrote:
>
>
> On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham wrote:
>
>> On 29/03/2011 4:54 AM, Sai Pooja wrote:
>>
>> There was a typo in the mail:
&g
On Mon, Mar 28, 2011 at 6:39 PM, Mark Abraham wrote:
> On 29/03/2011 4:54 AM, Sai Pooja wrote:
>
> There was a typo in the mail:
> E_protein-protein = Potential - E_water-water - E_protein-water
>
> On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja wrote:
>
>> Hi,
>>
There was a typo in the mail:
E_protein-protein = Potential - E_water-water - E_protein-water
On Mon, Mar 28, 2011 at 11:55 AM, Sai Pooja wrote:
> Hi,
>
> I have tried to implement a variant of Replica exchange called REST using
> gromacs. In REST, the potential energy is s
Hi,
I have tried to implement a variant of Replica exchange called REST using
gromacs. In REST, the potential energy is scaled in the following manner:
For the nth replica:
E_n = E_protein-protein + a_n * E_protein-water + b_n * E_water-water
I used tables to implement this. Separate tables for
Hi,
I am running a simulation for capped alanine dipeptide and I now need to
extract the dihedral angles. However, one of the nitrogen is named NT
instead of NH due to which g_rama is not able to give the dihedral angles.
Is there any other program I can use to get dihedral angles? I tried g_dih
a
Hi,
In Manual 4.5.3, the potential for dihedral restraints is the following:
Phi* = (Phi - Phi0)MOD 2Pi
Where Phi is the instantaneous dihedral and Phi0 is the reference dihedral.
And the MOD2Pi, I assume, ensures a difference <2Pi.
The Potential is: V=0.5*K*(Phi* - Phi0 -deltaPhi)**2
On Wed, Feb 2, 2011 at 6:49 PM, Sai Pooja wrote:
> Thanks Justin for being so patient. I have understood almost everything and
> I hope this is the last question on this thread.
>
> See inline ...
> On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul wrote:
>
>>
>>
Thanks Justin for being so patient. I have understood almost everything and
I hope this is the last question on this thread.
See inline ...
On Wed, Feb 2, 2011 at 5:53 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
> On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham > mark.
On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham wrote:
> On 3/02/2011 6:15 AM, Sai Pooja wrote:
>
>> The problem is solved with grompp i.e. I use the -t .cpt option. However,
>> now appending does not work. I remember Mark said in a previous mail that a
>> certain enviro
The problem is solved with grompp i.e. I use the -t .cpt option. However,
now appending does not work. I remember Mark said in a previous mail that a
certain environment variable can allow appending to happen even in such
cases. I would liek to try that out.
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For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
On Tue, Feb 1, 2011 at 1:04 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> I am doing a manual replica exchange(generalized hamiltonia
ma is clear now.
Pooja
On Tue, Feb 1, 2011 at 11:42 AM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> From the website:
>> "If you change the integrator or ensemble, you should pass the checkpoint
>> file to tpbconv only, not to mdrun, since the stat
... does this assure that the simulations start from the
coordinates/velocities specified by the .cpt file?
Pooja
On Tue, Feb 1, 2011 at 11:20 AM, Sai Pooja wrote:
> Thanks Mark. So if the simulation doesn't start from the checkpoint file,
> from where are the initial coordinates ve
Mark Abraham wrote:
> On 1/02/2011 7:50 AM, Sai Pooja wrote:
>
> I think I have figured out the reason. It is because I am carrying out
> replica exchange (manual) after every mdrun. If the exchange occurs, I
> exchange the checkpoint files, extend the simulation by 500 steps and
every 100ps?
Pooja
On Sat, Jan 29, 2011 at 6:52 PM, Mark Abraham wrote:
> On 30/01/2011 10:39 AM, Sai Pooja wrote:
>
> I would be happy to supply more information.. if someone could please look
> into this.. otherwise I will have to switch to storing every file and then
> just con
and starts from the point where the previous run
ended, can I be assured that an exchange has been affected - since tpr files
correspond to the "replica-box" and cpi to the most recent exchanged
replicas?
Pooja
On Mon, Jan 31, 2011 at 2:33 PM, Sai Pooja wrote:
>
> I manually
I would be happy to supply more information.. if someone could please look
into this.. otherwise I will have to switch to storing every file and then
just concatenating them which seems like a rather roundabout way of doing
it.
On Fri, Jan 28, 2011 at 4:37 PM, Sai Pooja wrote:
> This is
, Mark Abraham wrote:
> On 29/01/2011 3:56 AM, Sai Pooja wrote:
>
>> Hi,
>> I am using tpbconv and mdrun to extend a simulation. I use it with the
>> append option but the files still get overwritten or erased. Can someone
>> help me in this regard?
>> Pooja
>>
Hi,
I am using tpbconv and mdrun to extend a simulation. I use it with the
append option but the files still get overwritten or erased. Can someone
help me in this regard?
Pooja
Commands (in python)
cmd = '(%s/tpbconv -extend %f -s rex_%d.tpr -o rex_%d.tpr)'
%(GROMPATH,dtstep,i,i)
os.syst
Hi,
I am interested in carrying out umbrella sampling for a protein in explicit
solvent with the charmm forcefield. I want to impose a harmonic potential in
the dihedral space of only some specific atoms in the protein molecule. I am
having trouble figuring out a way to apply this using gromacs. C
Hi,
Is there a way to extract the attractive and repulsive parts of the LJ
interactions in a simulation?
Pooja
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Hi,
I am running a script that uses mdrun of gromacs and does replica exchange
(not using -replex). The reason is that I want to use different table files
for different replicas. However, it seems that I cannot supply unique table
names. For example, if I supply a table name different from
table_P
AM, Sai Pooja wrote:
>
>> Hi,
>> I run a simulation of a protein in water(tip3p) system using charmm
>> forcefield. I have specified the following energy groups:
>> Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype
>> to User and VdW t
Hi,
I run a simulation of a protein in water(tip3p) system using charmm
forcefield. I have specified the following energy groups:
Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype
to User and VdW to Cut-off. I then generate tables as specified in the
manual. To test the va
Hi,
I have scaled the non-bonded parameters(charges and epsilon) of tip3p atoms
in ffnonbonded.itp file(charmm forcefield). They are scaled by a ratio of
3/5. The simulation is then run at 500K for the protein water system. The
temperature exploded after first 20 steps. This does not happen if I r
Thanks Justin. I was just making sure that I was modifying the relevant
files.
On Thu, Nov 4, 2010 at 2:17 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> When using the charmm forcefield, the following is the case:
>> 1. ffnonbonded.itp - has listed paramters fo
When using the charmm forcefield, the following is the case:
1. ffnonbonded.itp - has listed paramters for tip3p (and other water models)
OWT3 and HWT3
2. ffbonded.itp - does not have paramters for OWT3 and HWT3
Does this mean:
1. nonbonded parameters for tip3p are read from ffnonbonded.itp for
Hi,
I am running a the gromacs Replica exchange (NVT). However along with the
temperatures, I have also scaled a few paramters in the topology file for
each of the replicas for generating the .tpr files. Everything seems to be
running fine but is this a valid thing to do? Or would gromacs simply i
. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> Restating that I was trying to scale the Protein Solvent interactions, I
>> added a new section to the ffnonbonded.itp file. This is what the section
>> looks like
>>
>> [ nonbond_params ]
&g
Hi,
Restating that I was trying to scale the Protein Solvent interactions, I
added a new section to the ffnonbonded.itp file. This is what the section
looks like
[ nonbond_params ]
C OWT31 0.00335276 0.0518
CA OWT31 0.00266209 0.0411
CC OWT3
On Thu, Oct 28, 2010 at 10:57 PM, Mark Abraham wrote:
> On 29/10/2010 10:14 AM, Sai Pooja wrote:
>
>> Hi,
>> I want to modify the contribution to Interaction energy of different
>> groups - say I have groups A and B and I want the energy to be scaled as
>> E_AA + 0
I have a follow-up question:
On Thu, Oct 28, 2010 at 10:57 PM, Mark Abraham wrote:
> On 29/10/2010 10:14 AM, Sai Pooja wrote:
>
>> Hi,
>> I want to modify the contribution to Interaction energy of different
>> groups - say I have groups A and B and I want the energy
vent temperatures as the biggest problem here.
>
>
>
> Quoting Mark Abraham :
>
>
>>
>> - Original Message -
>> From: Sai Pooja
>> Date: Monday, November 1, 2010 10:24
>> Subject: Re: [gmx-users] LINCS vs SHAKE
>> To: Discussion list for GR
ing the thermostat yet? Can you determine if the
> malformed residues are a result of a recent replica exchange? This continues
> to sound like an overheat that the thermostat cannot handle.
>
>
>
>
>
>
>
> Quoting Mark Abraham :
>
>
>>
>> -
sidechain are in incorrect positions(usually clashing). There doesn't seem
to be a good way of analyzing this error. If you have any suggestions I
would be eager to try them.
Pooja
On Sat, Oct 30, 2010 at 3:40 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>>
>
For Replica exchange, is there any advantage of in using SHAKE over
LINCS(other than the stepsize)?
I am running an REM simulation and the simulation stops after running for
variable number of steps (10, 1000 etc.) because some bond moves
more than 30 degrees and LINCS gives a warning.
P
Thanks Marks! That was very informative. When I try any/all of these I would
post the results.
Pooja
On Thu, Oct 28, 2010 at 10:57 PM, Mark Abraham wrote:
> On 29/10/2010 10:14 AM, Sai Pooja wrote:
>
>> Hi,
>> I want to modify the contribution to Interaction energy of differe
Hi,
I want to modify the contribution to Interaction energy of different groups
- say I have groups A and B and I want the energy to be scaled as E_AA +
0.1E_AB + 0.5*E_BB. Interaction parameters of each of these groups are set
by a forcefield
Now after multiple correspondence on the gromacs list
Hi,
While using trjconv I get this error:
VMD_PLUGIN_PATH not set. Using default location:
/usr/local/lib/vmd/plugins/*/molfile
No VMD Plugins found
Set the environment variable VMD_PLUGIN_PATH to the molfile folder within
the
VMD installation.
The architecture (e.g. 32bit versus 64bit) of Groma
On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Wednesday, October 27, 2010 8:52
> Subject: Re: [gmx-users] Forcefield parameters
> To: Discussion list for GROMACS users
>
> > On Tue, Oct 26, 201
On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>
>>
>> On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sai Pooja wrote:
>>
>>
On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Hi,
>> I want to change the non-bonded parameters to modify the interaction
>> between water molecules and protein molecules.
>> I am using CHARMM forcefield with Tip3p wa
Hi,
I want to change the non-bonded parameters to modify the interaction between
water molecules and protein molecules.
I am using CHARMM forcefield with Tip3p water.
The ffnonbonded.itp file of the forcefield has non-bonded parameters for
tip3p water. Can I achieve the above by changing these p
GROMACS 4.5 with charmm.
So one solution could be to open the output pdb file in a software like
Pymol, correct the coordinates and then make changes in the .gro file? Or do
I also need to edit the other files?
Pooja
On Tue, Oct 26, 2010 at 1:29 AM, Pär Bjelkmar wrote:
> Hello,
>
> > I use pdb
Hi,
I use pdb2gmx command to convert a pdb file to a .gro and .top file(using
CHARMM forcefield). For the C terminus, I use the CT3 option which is NCH3.
When I use editconf to get a pdbfile from the .gro file generated, the C=0
and the NCH3 seem to clash in space in pymol.
Is there a way of cor
Hi all,
I am using CHARMM forcefield with tables for Protein SOL interactions for
alanine dipeptide.
Tables supplied: table.xvg, table_Protein_SOL.xvg, tablep.xvg (Standard
tables for 6-12 interactions used)
Combination rule changed from '2' to '1' in forcefield.itp file.
In the energy minimizati
haps give us to enable people more
> knowledgeable than me to help.
>
>
> On 24/09/10 17:33, Sai Pooja wrote:
>
>> I use combination rule 1; but I also define all tabulated interactions for
>>> all possible *pairs* under the [ nonbond_params ] section, so the
>>
Hi,
Clarifications inline...
On Wed, Sep 22, 2010 at 2:01 PM, ms wrote:
> On 21/09/10 20:45, Sai Pooja wrote:
>
>> I wanted to change the interactions between the Protein and Solvent so I
>> tried using tables with the potential function scaled by a constant value.
>> I
Hi,
I wanted to change the interactions between the Protein and Solvent so I
tried using tables with the potential function scaled by a constant value. I
wanted to use this in combination with forcefield parameters (charmm). I
changed the combination rule in the forcefield.itp file from '2' to '1'
University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9909 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [ma
University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9909 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> *From:* gmx-users-boun...@gromacs.org [ma
Hi,
I am running an npt simulation on alanine dipeptide in explicit solvent
using charmm forcefield and tip3p.
The pressure is set to 1bar and the barostat is Parrinello-Rahman. The
simulation has been running for 45 ns and has not achieved the target
average pressure of 1 bar.
I don;t understan
Thanks Mark :).
On Tue, Sep 7, 2010 at 10:06 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Sunday, September 5, 2010 8:19
> Subject: [gmx-users] Tables and forcefield parameters
> To: Discussion list for GROMACS users
>
> > H
Hi,
ques1:
I have 3 energy groups.
I am interested in using tables for LJ and coulomb interactions for
Group1-group2 interactions.
For all other interactions:
1) Group1-group1 -all interactions-bonded and non-bonded
2) Group2-group2 -all interactions -bonded and non-bonded
3) All possible combina
Questions inline...
On Mon, Aug 30, 2010 at 7:25 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Tuesday, August 31, 2010 2:45
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users
>
> >
> > Tha
010 at 7:25 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Tuesday, August 31, 2010 2:45
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users
>
> >
> > Thanks Mark. I have just 2 more queries rega
--- Original Message -
From: Sai Pooja
Date: Monday, August 30, 2010 3:33
Subject: Re: [gmx-users] LJ potential
To: Discussion list for GROMACS users
> Hi,
>
> I am simulating a system of a protein in water. I am trying to run the
simulation with a modified protein-water LJ and coul
:54 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Sai Pooja
> Date: Monday, August 30, 2010 3:33
> Subject: Re: [gmx-users] LJ potential
> To: Discussion list for GROMACS users
>
> > Hi,
> >
>
> > I am simulating a system of a prot
; Hash: SHA1
>
> On 08/24/2010 02:27 PM, Sai Pooja wrote:
> > Hi,
> >
> > If there are n types of atoms in protein, how does one specify:
> > 1) Different types of LJ non-bonded interactions for different pairs?
> > 2) Modified Coloumb(by a pre-multiplier) i
Hi,
If there are n types of atoms in protein, how does one specify:
1) Different types of LJ non-bonded interactions for different pairs?
2) Modified Coloumb(by a pre-multiplier) interactions for different pairs?
Pooja
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Hi,
I used the git version of gromacs_with_charmm27_forcefield_nocmap(June, 20,
2010) to generate .gro and .top files. I then used these files on
gromacs-4.07 by copying the charmm27-ff library to my working directory.
Since I was not using cmap, gb and nucleic acid and lipids I deleted those
file
229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
>
> On Wed, Jul 21, 2010 at 1:38 PM, Sai Pooja wrote:
>
>> Thanks Rodrigo. I have read the paper and and I am familiar with the
>> topolog
al Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
> Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5
>
>
> On T
Thanks. You are right I tested it :).
On Tue, Jul 20, 2010 at 9:24 AM, ms wrote:
> On 19/07/10 17:25, Sai Pooja wrote:
>
>> Thanks Lanyuan.
>>
>> Can one use fewer processors than the number of replicas?
>>
>>
> My 0.02 £: I never did REMD, but, as far as
Hi,
If one has to make a version of gromacs charmm compatible, which files from
the charmm compatible version must be looked at?
Pooja
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Ple
Thanks Lanyuan.
Can one use fewer processors than the number of replicas?
Pooja
On Mon, Jul 19, 2010 at 12:18 PM, Lanyuan Lu wrote:
> No. For GMX4 each replica can be run on multiple processors.
> Lanyuan
>
> On Mon, Jul 19, 2010 at 10:36 AM, Sai Pooja wrote:
>
>> Hi,
Hi,
I would like to know if the Number_of_processors must be =
Number_of_replicas?
Regards
Pooja
--
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Please search the archive at http://www.g
Hi,
I am running an npt simulation for a protein in water. For more than 50% of
the residues the backbone atoms have been restrained by applying
posrestraints. I ran g_rmsf to check if the pos-restraints were working
well. When I do this selecting 'backbone' from the groups menu, my rmsf file
give
17, 2010 at 11:16 AM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> A charge grp consisting of 12 atoms is created from Arginine residues in
>> my topology file.
>> ; residue 14 ARG rtp ARG q +1.0
>> 476NH1 14ARG N150
O -0.51 4
On Sat, Jul 17, 2010 at 9:17 AM, Sai Pooja wrote:
> A charge grp consisting of 12 atoms is created from Arginine residues in my
> topology file.
>
> ; residue 14 ARG rtp ARG q +1.0
>476NH1 14ARG N150 -0.47 14.007
A charge grp consisting of 12 atoms is created from Arginine residues in my
topology file.
; residue 14 ARG rtp ARG q +1.0
476NH1 14ARG N150 -0.47 14.007 ; qtot
-3.47
477 H 14ARG HN150 0.31 1.008 ; qtot
-3.16
478
If gromacs assumes the aminoacid residues as charge groups by default then I
have many residues which have 12 atoms since I am using an all-atom force
field-charmm27(counting H).
Is there a way to define charge groups?
On Sat, Jul 17, 2010 at 7:41 AM, Justin A. Lemkul wrote:
>
>
>
:25 AM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> This is the .mdp file that produces notes-3 and 4. However, the previous
>> md file produces note-3.
>>
>> ; RUN CONTROL PARAMETERS
>> integrator
PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> I am trying to reproduce results from a paper which uses this cutoff. The
>> work is on loop-folding and they use implicit solvent. I am using explicit
>> solvent with charmm 27. Below is
, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> I am getting these notes when I run grompp:
>>
>> NOTE 3 [file Init/ffsb_init.top]:
>> The largest charge group contains 12 atoms.
>> Since atoms only see each other when the centers
rlist (2.00) - rvdw (2.00)
Can someone tell me how to correct these?
Pooja
On Thu, Jul 15, 2010 at 7:06 PM, Sai Pooja wrote:
> Hi,
>
> NOTE 4 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]:
> The sum of the two largest charge group radii (0.510406) is larger th
Hi,
NOTE 4 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]:
The sum of the two largest charge group radii (0.510406) is larger than
rlist (2.00) - rvdw (2.00)
NOTE 5 [file /fs/home/sm868/llamapooja/ffsb/Setup/nvt.mdp]:
The sum of the two largest charge group radii (0.510406) i
wrote:
>
>
> Sai Pooja wrote:
>
>>
>> 1. Pressure
>> For my initial configuration, I run a long nvt run. This gives me a
>> pressure. Then I run an npt simulation at this prerssure.
>> The idea is to do expansion runs(decrease pressure so that the system
>>
unning simulations for a planar system?
Pooja
On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>
>
>
> Do you run any equilibration prior to applying these parameters?
>> Both N-H and P-R allow for wide fluctuations in temperat
Reply inline...
On Thu, Jul 15, 2010 at 9:54 AM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Reply inline...
>>
>>
>> On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sai
Hi,
I am aware there have been many threads on this topic and I have looked at
some of them. I would still like to make this query. I am running an npt
equilibration run for a solvated protein using Charmm27-Tip3p (nocmap). I
ran the simulation for 1ns. The average values of pressure converge to 1
Reply inline...
On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> I have a system of 3600 LJ particles in a plane (using freeze-dimension
>> option in z). I am running npt runs using Semi-isotropic pressure couplin
Hi,
I have a system of 3600 LJ particles in a plane (using freeze-dimension
option in z). I am running npt runs using Semi-isotropic pressure coupling
with Parrinello-Rahman barostat. I have a few concerns:
1) On the gromacs website, a webpage mentions that this type of pressure
coupling may not
make &>log
310 ls
311 jmacs log
312 grep "error" log
313 grep "Error" log
314 make install
Pooja
On Sun, Jun 20, 2010 at 2:17 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> For future reference, I was able to install gromacs an
Now I use genion and it says no ions to add?
Using a coulomb cut-off of 1 nm
No ions to add and no potential to calculate.
command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o
solions.gro -p finalnoss.top
On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja wrote:
> I checked topol
I checked topology file but going with grompp makes sense. Thank you.
On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul wrote:
>
>
> Sai Pooja wrote:
>
>> Well thats the thing. I have checked my pdb files. All residues have
>>
>
> There aren't charges in a .pd
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