Use editconf -renumber on the starting structure and re-generate from that?
Mark
On Thu, May 23, 2013 at 5:45 AM, Kieu Thu Nguyen wrote:
> Dear all,
>
> I want to renumber residue number in file .top (to begin from 1). Have
> anyone has a script for this purpose ?
>
> Thankful for any help!
> T
Look at those files. Use diff. They're all the same. Your plots are
probably all showing the first column of each. You want to look at each
column. (And even then the best it can show is that your simulation is not
clearly inadequate.)
Mark
On Thu, May 23, 2013 at 8:48 AM, bharat gupta wrote:
>
Dear Sir,
Thank you for your reply. But I used the command demux.pl md$.log , where
$= No. of replica. I get the same plot every time. Sorry to ask this , but
where am I going wrong ??
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http://dx.doi.org/10.1021/ct300688p is probably very useful here.
Mark
On Thu, May 23, 2013 at 4:29 AM, Trayder Thomas
wrote:
> Thanks Mark,
> That really helped to clarify how everything is interacting around the
> verlet scheme.
> What statistics do you recommend examining between nstpcouple
On Wed, May 22, 2013 at 2:19 AM, bharat gupta wrote:
> Dear Sir,
>
> I performed another round of trial with different set of temperature and I
> got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
> 250 268 288 308 331 355 380 408 438 469 503 540 579 621
>
> I then checked
Dear all,
I want to renumber residue number in file .top (to begin from 1). Have
anyone has a script for this purpose ?
Thankful for any help!
Thu
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Hi Maggin,
It depend on your protein stability..It can be short or long..Check
the .edr file by using g_energy
On Thu, May 23, 2013 at 9:44 AM, maggin [via GROMACS]
wrote:
> Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need
> for NVT and NPT?
>
> ___
Thanks Mark,
That really helped to clarify how everything is interacting around the
verlet scheme.
What statistics do you recommend examining between nstpcouple settings?
Pressure/box size variation is the obvious one but I was curious whether
you had something else in mind.
-Trayder
On Thu, May
Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need
for NVT and NPT?
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I have used the program "g_density" to generate the mass density profile and
the charge density profile of molecules at gas-liquid interface. My question
is: Is the center of mass/charge used by g_density to compute the the
mass/charge density profile?
I'm eager for the answer, because the rev
Dear Sir,
I performed another round of trial with different set of temperature and I
got the avg accp. ration around 0.22. Here's the temp. dist. that I used :
250 268 288 308 331 355 380 408 438 469 503 540 579 621
I then checked the replica_index and replica_temp files for each replica
individu
On Wed, May 22, 2013 at 8:05 PM, rajat desikan wrote:
> Thanks for the reply,
> trjconv does not have any bugs in removing pbc, right? We can just feed the
> -nojump output to g_msd.
>
Maybe. There are not (yet) any automated tests for the code in these tools.
But probably trjconv -nojump works c
On Wed, May 22, 2013 at 6:32 AM, Trayder wrote:
> Hi all,
> I've been running 5fs timestep simulations successfully without gpus
> (united-atom, HEAVYH). When continuing the same simulations on a gpu
> cluster
> utilising the verlet cutoff-scheme they crash within 20 steps. Reducing the
> timeste
Thanks for the reply,
trjconv does not have any bugs in removing pbc, right? We can just feed the
-nojump output to g_msd.
I am going to output the coordinates and velocities with g_traj and run it
through my own code :)
On Wed, May 22, 2013 at 11:19 PM, Mark Abraham wrote:
> Along the lines of
Along the lines of take a trajectory, and look through it for a frame where
it crosses the periodic boundary of the original cell. Look for artefacts
in the analysis at that time. Or take that frame and use it as a reference
state for whatever trjconv-based PBC-massaging workflow you previously use
Hi Mark,
Regarding your statement, how does one check whether g_msd has removed pbc
correctly or not?
Thanks
On Wed, May 22, 2013 at 10:56 PM, Mark Abraham wrote:
> On Wed, May 22, 2013 at 4:49 PM, Yutian Yang wrote:
>
> > Erik,
> >
> > Do you mean that if the particle diffuses too fast, it wil
On Wed, May 22, 2013 at 4:49 PM, Yutian Yang wrote:
> Erik,
>
> Do you mean that if the particle diffuses too fast, it will appear like it
> doesn't move because of the PBC?
>
Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect
I have another issue. If I have a polymer chain with the length
lloyd riggs wrote
>
>
> Dear Andrish Reddy,
>
>
>
> Dont know if it works but I have for small molecules just put all the
> parmeters within the .top file right below the defaults, instead of user
> defined tables, and removed the "forcefieldX/SPC.itp" or
> equivalent section so it doesn't
Hi,
I'm trying to understand how best to compare performance of Gromacs 4.6.1 on
CPU only versus CPU plus GPU on a cluster. Each node has is 2 x 8 Core Sandy
Bridge + 1 Nvidia M2090.
I've been trying to use the d.dppc benchmark (with modifications). I would
like to profile both standard cutoff an
Dear Andrish Reddy,
Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the "forcefieldX/SPC.itp" or equivalent section so it doesn't loop, but dont know if it works in your
Erik,
Do you mean that if the particle diffuses too fast, it will appear like it
doesn't move because of the PBC?
I have another issue. If I have a polymer chain with the length almost the same
as the box length. It is possible that the COM diffusion of the chain may
appear it does not move
Dear all,
I am trying to use g_velacc to calculate diffusion coefficient for a single
polymer chain. As I follow the Gromacs tutorial and use the command (version
4.5.1)
g_velacc -acflen 1001 -nonormalize -mol -n atoms.ndx -s topol.tpr
the ACF is always zero. However, if I remove -mol option,
Dear all,
We have 80 polymers in the simulation box, for some reason, we want to make the
COM of each polymer be fixed. Is this possible in Gromacs with any command, or
somewhere in the source code we can change the expression of displacement along
with time .
Thank you very much in advance.
Exactly a factor of ten? Angstrom vs nm issue?
On Wed, May 22, 2013 at 4:09 PM, Andrish Reddy wrote:
> Greetings,
>
> I am trying to use tabulated potentials for the VdW interactions between
> TIP5P water molecules.
> I have tested my topology file to make sure that it gives reasonable
> result
Arunima Shilpi-2 wrote
> Respected sir
>
> I want to calculate the distance between protein and ligand after I have
> run the production step. I used the following command..
>
> g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx
>
> Groups I selected was
> Group 1 (protein)
> Group 13
Greetings,
I am trying to use tabulated potentials for the VdW interactions between
TIP5P water molecules.
I have tested my topology file to make sure that it gives reasonable results
with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 ,
C12=4*eps*sig^12. I am able to match the
Use gmxcheck to find out what's in the files. Think about how you used
xtcgroups. Consider using tpbconv to make a matching subset from your .tpr.
Mark
On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi wrote:
> Respected sir
>
> I want to calculate the distance between protein and ligand after I
Sure. What's the MSD of a pendulum if you only sample at a rate equal to
the period? How often you want to sample depends on the time scale of what
you want to observe. That might be up to you to measure :-)
Mark
On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina <
anna.akinsh...@manchester.ac.uk>
Hi,
For particles that diffuse more than half a box length between frames will
appear as if they haven't moved much, assuming you have periodic boundary
conditions.
Erik
On 22 May 2013, at 11:41, Anna Akinshina
wrote:
> Dear Gromacs Users,
>
> I have a question interpreting obtained msd da
Hi, if I want to calculate the free energy of solvation of peptide, because
both van der Waals and Coulombic interactions are important for peptide
so I set couple-lambda0 = none
couple-lambda1 = vdw-q
is it right?
or it's better to choose wo-stage approach to do this work:
van der
Respected sir
I want to calculate the distance between protein and ligand after I have
run the production step. I used the following command..
g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx
Groups I selected was
Group 1 (protein)
Group 13 (ligand)
It says the following error
Mole
Dear Gromacs Users,
I have a question interpreting obtained msd data.
I need to calculate diffusion coefficient for a single argon atom in a box of
water (500 molecules).
During the calculations (50ns) I write both trr and xtc trajectories, but to
save space I write trr for whole system very sel
Dear all,
I
want to simulate a system consisting of cholesteryl ester. I have to
use charmm27 all atom force field for which I am not able to get the
parameters. I tried using lipid book but did not find any files. As I am
a new beginner to performing simulations, I have no idea about other
so
g_hbond and g_hbond -contact
Erik
On 22 May 2013, at 05:37, Vishal Kumar Jaiswal wrote:
> Hello gromacs users
>
> I performed a 1 ns simulation of N-isopropylamide in water. Now i wish to
> calculate the average no of water molecules(averaged over entire
> trajectory) within a certain distance
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