While, is it needed to list all the possible interacting (two) atoms
in the energygrp_table
option? I have more than 3000 possible two-atom pairs, corresponding to
more than 3000 table_*.xvg files.
On Wed, Nov 30, 2011 at 12:29 AM, Mark Abraham wrote:
> On 30/11/2011 5:25 PM, Liu, Liang wr
The error shows as "An input file contains a line longer than 4095
characters, while the buffer passed to fgets2 has size 4095."
On Wed, Nov 30, 2011 at 12:22 AM, Mark Abraham wrote:
> On 30/11/2011 5:09 PM, Liu, Liang wrote:
>
> Dear all,
>
> I am trying to use t
Dear all,
I am trying to use tabulated potentials in my simulation. However, there is
a limit on energygrp_table and the grompp reports error.
The interaction happens between any two of atoms, and their might be more
than 3000 possible couples.
What should I do to remove the limit? Thanks.
--
Be
Dear all,
Assuming I have a some tabulated potentials, table.xvg, tablep.xvg,
table_P_P.xvg, table_P_C.xvg and so on.
Also there are non-zero values in the first column of both table.xvg and
tablep.xvg; while the first column (x), the six column (h(x)) and the last
column (h'(x)) have non-zero num
wrote:
>
>
> Liu, Liang wrote:
>
>> Well, I already have the xvg files from others. However I don't know how
>> to use it.
>>
>>
> Start with the manual, where modifications to the topology and relevant
> commands and files are described. Then r
Well, I already have the xvg files from others. However I don't know how to
use it.
On Thu, Nov 17, 2011 at 10:00 AM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Dear all,
>>
>> I am trying to calculate potentials for RNA structures with a serial of
Dear all,
I am trying to calculate potentials for RNA structures with a serial of
tabulated potentials (non-bonded).
And the only potential I am going to use is the tabulated potentials, and
the effect from force field should be removed.
However, when I use pdb2gmx to build the topology file, I ha
Dear all,
I am wondering if there is a way to calculate the potential of a given RNA
structure? No minimization, no simulation, but calculate the potential.
--
Best,
Liang Liu
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search th
Thanks, I will try to figure it out.
On Tue, Nov 15, 2011 at 9:50 PM, Mark Abraham wrote:
> On 16/11/2011 2:45 PM, Liu, Liang wrote:
>
> Thanks for help.
> If I have more atoms and they can interact each other or itself, like PP,
> PC, PN, CP, CN, CC How's the energygr
P P P C
>
>
>
> so now mdrun looks for table_P_P.xvg and table_P_C.xvg in the run
> directory, and uses it for P-P and P-C interactions, whereas for all other
> interactions default table.xvg file is used.
>
>
> I hope this helps.
>
> Regards
> Sikandar
>
>
I am trying to use a serial of tabulated potentials, which are the
functions of the distance between atoms and the names are table.xvg,
table_P_P.xvg, table_C_P.xvg, etc., to do the energy minimization of some
RNA structures.
The procedure I apply is as following:
pdb2gmx -f rna.pdb -o conf.pdb -f
The tabulated potentials I am using is non-bonded interactions. The
question is the application of these potentials will only modify the force
field, e.g. amber03, or will take place of the force field?
On Mon, Nov 14, 2011 at 6:40 PM, Mark Abraham wrote:
> On 15/11/2011 9:33 AM, Liu, Li
Yes, I found it. THanks.
On Mon, Nov 14, 2011 at 9:45 PM, Terry wrote:
>
> This is what you are looking for:
>
>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting
>
> Terry
>
>
> On Tue, Nov 15, 2011 at 11:42 AM, Liu, Lia
I am wondering if there is a flag to make the command select SOL
automatically instead of pressing some number each time? I have thousands
of structures, it is really time-consuming to select one by one.
--
Best,
Liang Liu
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.o
I have a serial of tabulated potentials with the name of *.xvg, which are
the function of atom distance.
I am wondering how to use them in gromacs simulation? Will that replace the
force field, e.g. amber03? Thanks.
--
Best,
Liang Liu
--
gmx-users mailing listgmx-users@gromacs.org
http://lis
Thanks.
Do you know how to use a new force field, not amber or charm, but a force
field built by someone else, and it's already in Gromacs format (tons of
xvg file, right?)
On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> This i
d to check the "NOTE" of "System has non-zero total charge" in the
output of grompp command? And also update the topology file automatically
too?
On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Hi, all,
>&g
Hi, all,
I am wondering if Gromacs can do the following work?
Assuming I have a pdb file of an RNA molecule. Some atoms may be too close
or even overlap, I am wondering if Gromacs can move the atoms to reasonable
positions and remove the bad contacts? The final structure is supposed to
be the "mos
Well, the thing is even I turn off the position restraint and raise the
temperature to 600k, the RMSD I can obtained is only about 0.3 for a RNA
hairpin.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.
you want
> to have broader sampling, raise the temperature or add denaturants.
> But also ask yourself the question if what you think you want is what
> you should be wanting. What is the actual question you're trying to
> solve?
>
> Cheers,
>
> Tsjerk
>
> On Mon
How's position restraint? If the force constant is reduced (reduce the
number in posre.itp ?), the simulation will lead to more flexible structure?
On Mon, Oct 10, 2011 at 10:20 AM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Thanks.
>>
>> Wi
Thanks.
Will the constrain help?
On Mon, Oct 10, 2011 at 10:06 AM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Hi, all,
>>
>> I am trying to use Gromacs to obtain structural ensembles around native
>> structures (PDB structures).
>> Howeve
Hi, all,
I am trying to use Gromacs to obtain structural ensembles around native
structures (PDB structures).
However the simulated structures are always very close to the initial one,
with RMSD < 0.2.
I am wondering how to obtain large-RMSD structures? Thanks.
--
Best,
Liang Liu
--
gmx-users m
, Sep 29, 2011 at 4:24 PM, Mark Abraham wrote:
> On 30/09/2011 2:50 AM, Liu, Liang wrote:
>
> After running for more than 12 hours, the REMD simulation is completed and
> what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
>
>
> Yep. One for each simulation.
>
>
&
After running for more than 12 hours, the REMD simulation is completed and
what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
Not sure if the result is reasonable.
I tried to analyze the result, and after applying demux.pl, two
files replica_index.xvg replica_temp.xvg are obtained.
My questi
After running for more than 12 hours, the REMD simulation is completed and
what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
Not sure if the result is reasonable.
I tried to analyze the result, and after applying demux.pl, two
files replica_index.xvg replica_temp.xvg are obtained.
My questi
Not know. I will update the result tomorrow, as the 5 steps take really
long time :(
On Wed, Sep 28, 2011 at 4:38 PM, Mark Abraham wrote:
> On 29/09/2011 7:20 AM, Justin A. Lemkul wrote:
>
>>
>>
>> Liu, Liang wrote:
>>
>>> Yes, they are updated like:
&g
84e-05
...
On Wed, Sep 28, 2011 at 4:08 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Thanks. currently what I see is the program runs very slowly, but get .log
>> file for all the 50 replicas, does this mean all of them are running?
>>
>>
> Are the l
Thanks. currently what I see is the program runs very slowly, but get .log
file for all the 50 replicas, does this mean all of them are running?
On Wed, Sep 28, 2011 at 3:41 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Well, although this makes sense, why all t
Well, although this makes sense, why all the 50 replicas are running when I
run "mpirun
-np 50 mdrun_mpi -s md.tpr -multi 50 -replex 50" on my own computer
with only 2 cores?
By the way, would you please show me where I can find the reasonable replex
number information in the literature? I
So if my personal computer have 2 cores, the np should be set to 2? Does it
relate to -multi?
How to choose a reasonable number for -replex? the smaller the better?
Thanks again.
On Wed, Sep 28, 2011 at 3:06 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> This w
, multi or replex?
Is the simulation time still set in the mdp file with nsteps and dt? e.g.
nsteps = 50 and dt = 0.002 to run a 1ns simulation?
Any helps will be highly appreciated.
On Wed, Sep 28, 2011 at 1:27 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> T
ot;. What is this for?
On Wed, Sep 28, 2011 at 1:02 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Does that mean I have to use MPI? I got an error "mdrun -multi is not
>> supported with the thread library.Please compile GROMACS with MPI support"
>
Does that mean I have to use MPI? I got an error "mdrun -multi is not
supported with the thread library.Please compile GROMACS with MPI support"
after run "mdrun -s md.tpr -multi 10 -replex 10"
On Wed, Sep 28, 2011 at 12:58 PM, Justin A. Lemkul wrote:
>
>
> Liu,
Hi everyone,
I tried to use Gromacs to run REMD simulation.
Firstly a set of (md#).mdp file are make and the grompp command can generate
the same amount of (md#).tpr file.
Assume # = 10,
then I tried to run REMD as mdrun -s md.tpr -np 10 -replex 10.
However, a fetal error shows as "Need at least t
Liu, Liang wrote:
>* > Thanks.*>* >*>* > Is this position restraint same to the
>one "Position Restrained*>* MD". I*>* > see some tutorial shows there
>are always three step to perform a*>* > simulation: Ene
It is weird why I always receive the digest of the mailing list but the
specific topic?
On Tue, Sep 27, 2011 at 9:14 AM, Liu, Liang wrote:
> > Thanks.
>> >
>> > Is this position restraint same to the one "Position Restrained MD". I
>> > see some tu
>
> > Thanks.
> >
> > Is this position restraint same to the one "Position Restrained MD". I
> > see some tutorial shows there are always three step to perform a
> > simulation: Energy minimization, Position Restrained MD and MD
> Simulation.
>
> "Always" is too strong, but this is common.
>
> > Is
Restrained MD? Thanks.
On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Firstly I want to thank for your reply, yes, it should be position
>> restraint.
>>
>> I don't know how to reply in the thread, actually that was
l E =
k(r-r0)^2, with different values of k?
I am totally a new user of Gromacs, even MD simulation. Please help, Thanks
a lot.
On Mon, Sep 26, 2011 at 4:56 PM, Justin A. Lemkul wrote:
>
>
> Liu, Liang wrote:
>
>> Firstly I want to thank for your reply, yes, it should be pos
I am running Gromacs for RNAs, and I got a problem during the simulation:
How to perform the simulation with each heavy atom constrained to its
initial position by a harmonic potential, E = k(r-r0)^2?
--
Best,
Liang Liu
--
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