Perhaps you need a less prehistoric compiler. Or the affinity-setting bug
fix in 4.6.3. Or both.
On Jul 17, 2013 6:25 PM, "Shi, Yu (shiy4)" wrote:
> Dear gmx-users,
>
> My problem is weird.
> My mdrun worked well using the old serial version 4.5.5 (about two years
> ago). And I have these top, n
Unfortunately, the semiiso fix for MTTK is not trivial, and will have
to wait until 5.0.
Berendsen volume + expanded ensemble would likely give very bad
results, especially since surface area fluctuations are important.
Replica exchange works with sd and parrinello-Rahman, if that helps!
I am wo
Dear gmxers,
By running the command g_hbond -ac, a resulting .xvg file is generated,
which is attached below. In that file, there are five columns. I guess
that, the first column is time, the second the HB autocorrelation function.
But what are the other columns denoted by s1, s2, s3? Thanks a lot
The test I did was using gmx-4.6.3. I'm currently working on a membrane
system, which requires semiisotropic pressure coupling. I know that MTTK in
gmx-4.6.3 doesn't support semiiso yet so the only combination available for
expanded ensemble is md-vv + v-rescale tcoupl + berendsen pcoupl, which I'm
> It seems to have something to do with the integrator/pressure-coupling.
that is what I expected based on some preliminary testing earlier.
When
> I ran the tutorial on
> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble,
> everything seems fine
OK go
4.5.7 does not support Hamiltonian exchange. It says all properties
are the same, because all the temperatures and pressures are the same
-- it won't switch the umbrellas.
On Wed, Jul 17, 2013 at 3:30 PM, Parisa wrote:
> Hi Michael,
>
> I think that this is an issue with the gromacs version I am
Hi Michael,
I think that this is an issue with the gromacs version I am using (4.6.1). I
switched to 4.5.7 and now, I get the error:
Fatal error:
The properties of the ... systems are all the same, there is nothing to
exchange
I don't understand what I am missing here. I suppose if I have 3 repl
You can also look them up (angles bond distances) in the CRC handbook or online and just put the angle(distances direct into the .itp file for your ligand, as well as impropers...it works for all the force fields, unless you use hybrids (CH3=1 representation)...it comes out wierd as the different
On Wed, Jul 17, 2013 at 4:09 PM, Jacopo Sgrignani wrote:
> Dear all
> I would like running a replica exchange simulation using gromacs and gpu.
> However when I Try to run the calculation I get this message
>
> mdrun -multi is not supported with the thread library.
REMD requires an MPI-enabled bi
On 7/17/13 2:15 PM, gromacs query wrote:
what you mean here about the improper being defined "about bonds."
Sorry I meant peptide bond itself
That's all there is to it.
Does that mean Yes and I understood it correctly or something else? sorry
about that!
Yes, what you posted is correct
>>what you mean here about the improper being defined "about bonds."
Sorry I meant peptide bond itself
>> That's all there is to it.
Does that mean Yes and I understood it correctly or something else? sorry
about that!
regards,
Jiom
On Wed, Jul 17, 2013 at 9:01 PM, Justin Lemkul wrote:
>
>
You tried ppn3 (with and without --loadbalance)?
Mark
On Wed, Jul 17, 2013 at 6:30 PM, gigo wrote:
> On 2013-07-13 11:10, Mark Abraham wrote:
>>
>> On Sat, Jul 13, 2013 at 1:24 AM, gigo wrote:
>>>
>>> On 2013-07-12 20:00, Mark Abraham wrote:
On Fri, Jul 12, 2013 at 4:27 PM, gigo
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 in the aminoacids.rtp file specify impropers
centered on the C and N atoms of the peptide bond.
I meant
It seems to have something to do with the integrator/pressure-coupling. When
I ran the tutorial on
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble,
everything seems fine unless I switched to sd integrator instead of md-vv
(and Pcoupl from MTTK to beren
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 in the aminoacids.rtp file specify impropers
centered on the C and N atoms of the peptide bond.
I meant to say its easy to define (in general) im
On 2013-07-13 11:10, Mark Abraham wrote:
On Sat, Jul 13, 2013 at 1:24 AM, gigo wrote:
On 2013-07-12 20:00, Mark Abraham wrote:
On Fri, Jul 12, 2013 at 4:27 PM, gigo wrote:
Hi!
On 2013-07-12 11:15, Mark Abraham wrote:
What does --loadbalance do?
It balances the total number of proce
Dear gmx-users,
My problem is weird.
My mdrun worked well using the old serial version 4.5.5 (about two years ago).
And I have these top, ndx, mdp, and gro files.
Basing on those old files, for the serial 4.6.2, the grompp works through,
resulting the .tpr file successfully.
After that when I m
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 confused (I have tried to explain below please let me know if I
have defined impropers correctly for
Dear Justin,
1) I can understand the improper for stereocenters (chiral) easily but with
bonds I am confused (I have tried to explain below please let me know if I
have defined impropers correctly for peptide to keep it planar).
H1 O H3
\ I /
--C1---C--N---C2--
On 7/17/13 10:54 AM, Sainitin Donakonda wrote:
I started MD very recently dont have much experience you said i would need
.tpr file which doesnot use PME ? how can i get that ?
By writing a new .mdp file that doesn't use PME. Please refer to previous
discussions on this topic. People ask
I started MD very recently dont have much experience you said i would need
.tpr file which doesnot use PME ? how can i get that ?
Thanks,
Nitin
On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul wrote:
>
>
> On 7/17/13 10:43 AM, Sainitin Donakonda wrote:
>
>> Ok..thanks...so i will use -rerun opti
Ok..thanks...so i will use -rerun option in final production ..step..as
follows...actually i ran 20 ns MD simulation so i used extend option to run
everything in cluster in correct time
#first 10 ns
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_10.tpr
mdrun -s MD_10.tpr
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/040125.html
I have few queries:
1) do I need to define improper f
On 7/17/13 10:43 AM, Sainitin Donakonda wrote:
Ok..thanks...so i will use -rerun option in final production ..step..as
follows...actually i ran 20 ns MD simulation so i used extend option to run
everything in cluster in correct time
#first 10 ns
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol
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)
On 7/17/13 10:12 AM, Sainitin Donakonda wrote:
Usually i collect data after final production run...after this i take .xtc
file and analyze it using various gromacs tools ..
And there you have it. LIE is just an analysis method like anything else.
There is no purpose in my mind in reanalyzi
Usually i collect data after final production run...after this i take .xtc
file and analyze it using various gromacs tools ..
thanks,
nitin
On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul wrote:
>
>
> On 7/17/13 9:21 AM, Sainitin Donakonda wrote:
>
>> Hi justin,
>>
>> Thanks for explaination ..
Dear all
I would like running a replica exchange simulation using gromacs and gpu.
However when I Try to run the calculation I get this message
mdrun -multi is not supported with the thread library.
how do I compile gromacs ?
Could anyone confirm me the possibility to run 8 replicas on one GPUs
On 7/17/13 9:21 AM, Sainitin Donakonda wrote:
Hi justin,
Thanks for explaination .. i already ran MD for both ligand alone and
protein ligand complex..
So now can you please tell me where should use mdrun -rerun option ..i mean
at which stage ..should i used in Energy miniminimzation or NVT
Hi again,
I can give more details about acpype error. This is the error that I
obtained,
===
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev:
389 (c) 2012 AWSdS |
=
Hi justin,
Thanks for explaination .. i already ran MD for both ligand alone and
protein ligand complex..
So now can you please tell me where should use mdrun -rerun option ..i mean
at which stage ..should i used in Energy miniminimzation or NVT and NPT
equilibration or Production run ..
Or sho
On 7/17/13 8:54 AM, Sainitin Donakonda wrote:
Hi ,
I want to use g_lie for my protein-drug complex to get binding energy ..i
read some information that we need take care some issues if we used PME
electrostatics..
Indeed i have used PME in my simulation..
Can any body explain which parameter
Hi ,
I want to use g_lie for my protein-drug complex to get binding energy ..i
read some information that we need take care some issues if we used PME
electrostatics..
Indeed i have used PME in my simulation..
Can any body explain which parameters to be taken care while running g_LIE
and what is
thank justin
>
>
> On 7/17/13 8:19 AM, pooja_gu...@nccs.res.in wrote:
>> i took only single structure
>>>
>
> You can't calculate entropy from a single structure. Please investigate
> the
> literature.
>
> -Justin
>
>>>
>>> On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote:
okk
This
On 7/17/13 8:19 AM, pooja_gu...@nccs.res.in wrote:
i took only single structure
You can't calculate entropy from a single structure. Please investigate the
literature.
-Justin
On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote:
okk
This may be very basic question.
I took a natural p
i took only single structure
>
>
> On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote:
>> okk
>>
>> This may be very basic question.
>> I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I
>> picked up one unfolded structure from the trj and solvated with water. I
>> ran em for fu
On 7/17/13 8:09 AM, pooja_gu...@nccs.res.in wrote:
okk
This may be very basic question.
I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I
picked up one unfolded structure from the trj and solvated with water. I
ran em for full system. now i am calculating the entropy. I a
okk
This may be very basic question.
I took a natural pdb and unfold with SAMD. I ran simulation for 10ns. I
picked up one unfolded structure from the trj and solvated with water. I
ran em for full system. now i am calculating the entropy. I afraid if i
missed something.
I am doing this first tim
try trjconv to extract the structures
pooja
> You can do it by using simple shell scripting
> On Jul 17, 2013 12:58 AM, "Shine A" wrote:
>
>> Sir,
>>
>> Using g_cluster I clustered snapshots in md trajectory using the
>> command as follows
>>
>> g_cluster -s sd_7.tpr -f traj7.trr -dist r
On 7/17/13 7:56 AM, pooja_gu...@nccs.res.in wrote:
I used system (0) for g-covar.
Most likely, g_anaeig is running out of memory. Try using some subset of the
system, like the protein only or its backbone.
-Justin
On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote:
thanks for reply
i
You can do it by using simple shell scripting
On Jul 17, 2013 12:58 AM, "Shine A" wrote:
> Sir,
>
> Using g_cluster I clustered snapshots in md trajectory using the
> command as follows
>
> g_cluster -s sd_7.tpr -f traj7.trr -dist rmsd-distribution.xvg -o
> clusters.xpm -sz cluster-sizes.
I used system (0) for g-covar.
Pooja
>
>
> On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote:
>> thanks for reply
>>
>> i am using Gromacs 4.5.5 version
>> command
>> g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp
>>
>
> What was the g_covar command used to generate the eigenv
On 7/17/13 7:42 AM, pooja_gu...@nccs.res.in wrote:
thanks for reply
i am using Gromacs 4.5.5 version
command
g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp
What was the g_covar command used to generate the eigenvector .trr file? What
group did you choose for analysis
thanks for reply
i am using Gromacs 4.5.5 version
command
g_anaeig -v *.trr -entropy -s *.tpr -extr -f *.pdb -rmsf -3d -comp
-Pooja
>
>
> On 7/17/13 7:28 AM, pooja_gu...@nccs.res.in wrote:
>> Hi Justin
>>
>> When i used g_anaeig option for the calulation, i choose system as an
>> option i got an
On 7/17/13 7:28 AM, pooja_gu...@nccs.res.in wrote:
Hi Justin
When i used g_anaeig option for the calulation, i choose system as an
option i got an error "Segmentation fault (core dumped)"
Please provide the exact sequence of commands you used, copied and pasted from
your terminal. Please a
Hi Justin
When i used g_anaeig option for the calulation, i choose system as an
option i got an error "Segmentation fault (core dumped)"
>
>
> On 7/16/13 4:30 AM, pooja_gu...@nccs.res.in wrote:
>> Hi gmx users
>>
>> I took a natural protein fold and unfolded with simulated annealing
>> molecular d
On 7/17/13 6:26 AM, Archana Sonawani-Jagtap wrote:
Hi Justin,
Thanks...it was really helpful. I saw the
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site.
Now I don't know how to calculate the number of cosolvents (in my case
TFE for TFE-water in 1:1 vol). Is there any formula
Hi Justin,
Thanks...it was really helpful. I saw the
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site.
Now I don't know how to calculate the number of cosolvents (in my case
TFE for TFE-water in 1:1 vol). Is there any formula to carry out this
calculation. I can follow other menti
No, indeed.
If Souilem had described their real objective then maybe they'd get
some actual help :-)
Mark
On Wed, Jul 17, 2013 at 11:10 AM, Justin Lemkul wrote:
>
>
> On 7/17/13 12:20 AM, Souilem Safa wrote:
>>
>> Dear Gromacs users,
>> Can anyone please help me how can I convert a cpt file fro
On 7/17/13 12:20 AM, Souilem Safa wrote:
Dear Gromacs users,
Can anyone please help me how can I convert a cpt file from a new to an
older Gromacs version?
There's no way to do that of which I'm aware.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Po
On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote:
HI,
I want to simulate helical peptide in TFE-water (1:1 vol) solvent.
1. From previous searches, I got to know that tfe.itp is present in
gmx.ff folder. Can I use this itp file by including it in my top file
generated during pdb2gmx.
Sinc
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