is high to about 0.5nm.
Can someone explain for me?
Sincerely yours,
Hsin-Lin
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Hi Mark,
Thank you for your reply.
I understand now.
Sincerely yours,
Hsin-Lin
I want to calculate the diffusion coefficient of a small polypeptide
with g_msd (see here
http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant)
because of periodic boundary condition, when the peptide
d run mdrun -nt 12 before?
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Hsin-Lin
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right
in the
file.
So I added -noappend to rerun it again and this result will be correct without
doubt.
By the way, md100ns.trr here mean from 50ns to 100ns.
I just don't want the new run append to md50ns.trr to make me confused.
Hsin-Lin
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Hi Flo,
Thank you for reply.
I got it.
But as you see I also indicate the new names for output files.
Do I get correct result in this kind of situation?
Or I need to rerun it with "-noappend"
Sincerely yours,
Hsin-Lin
>Hi,
>
>check the standard options of mdrun with the help
y get md100ns.trr, md100ns.gro, md100ns.edr, and
md100ns.log.
So, is the function of part number in extending simulation in ver.4.5.4
cancelled?
Hsin-Lin
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Hi Justin,
I understand now.
The vector of box changed from 5.8 to 44 after the short MD for equilibrium.
I don't know what happened during equilibrium.
But that is belong to the other question now.
Thank you very much for your reply.
Sincerely yours,
Hsin-LIn
> Hsin-Lin Chiang wrote:
se give me more messages in detail?
Hsin-Lin
---
Written by Emile Apol, Rossen
Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, Pär Bjelkmar, Rudi van
Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per
ltype = isotropic
;tau_p = 0.1
tau_p = 0.25
compressibility = 5.4e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529
Hsin-Lin
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.4e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529
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Hsin-Lin
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P
ltype =
isotropic
;tau_p
= 0.1
tau_p
= 0.25
compressibility = 5.4e-5
ref_p
= 1.0
gen_vel
= yes
gen_temp
= 300
gen_seed
= 173529
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Hsin-Lin
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Hi Tsjerk,
It's very helpful information.
Thank you very much
Sincerely yours,
Hsin-Lin
Hi
Hsin-Lin,
If you use a .tpr file, you perform a mass-weighted fit and
analysis.
A .gro file has no masses and thus the fit and analysis are
performed
non-mass weighted, which will give differ
for us to see whether you or GROMACS has done something
> wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do
> something else with our time :-)
>
> Mark
Hi,
I checked the result again
The order of the different is less than 0.1 nm.
So that means th
> On 17/08/11, Hsin-Lin Chiang wrote:
>
> > Hi,
> >
> > I got confused about the choice of reference structure of g_rms. (g_rms -s)
> > For example,
> > I run MD after PR.
> > That's means md.tpr was generated from pr.gro
> > I tried t
esult.
Could someone tell me what cause the different and which choice is better?
And my version is gromacs v4.0.5
Sincerely yours,
Hsin-Lin
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file the residue number is 1 to 21 and 1 to 30.
/>/
/>/ I'm afraid VMD got confused for the repeat number 1 to 21.
/>/ So I change 1-30 in b-chain to 22-51.
/>/ Then snapshot in VMD become correct.
/
Then this was primarily VMD's issue.
-Justin
Thank you for your hel
>/
/>>/ I doubt the chain identifiers are relevant. Both .gro and .pdb files
should
/>>/ display properly. The only odd instance I can think of is that without
separate
/>>/ chains, some programs may interpret the protein coordinates as a single
/>>/ molecule, but I would think that would
n handle this and I don't need to
separate chains manually.
Hsin-Lin
-Justin
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Please
, maybe the error of snapshot was just because chain identifiers were
lacked before.
Do I have any commend can use instead of chain identifier A and B mannually?
Sincerely yours,
Hsin-Lin
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Pleas
Hsin-Lin Chiang wrote:
>/ Hi,
/>/
/>/ I'm trying to heat a protein.
/>/ There are two chains, A-chain and B-chain.
/>/ Two disulfide bonds are between A-chain and B-chain.
/>/ As I know, I should let A-chain and B-chain belong to the same [molecule
/>/ type] in .
quot;the number of A-chain's residues plus 1".
And it was also strange that the number of first water molecules was
equal to "the number of B-chain plus 1"
I thought it should be equal to "the number of A-chain's residues plus
the number of B-chain's residues plus 1&
r topology.
-Justin
I understand now.
Thank you very much for your help.
Sincerely yours,
Hsin-Lin
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uot;
>(which should also work in this case) does not.
>
>-Justin
I get success in pdb2gmx, but I not only delete ter line but also all OXT lines
according to this mailing list,
http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html
But I'm failed when I used mdrun in &quo
log file.
I'm not sure if I can post all here.
Do we have another way to discuss?
Sincerely yours,
Hsin-Lin
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於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到:
Hi everyone,
>
> My pdb file is consist of two chains with one intra- two
> inter-disulfide bonds.
> So I used pdb2gmx in this way
> pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep ter
> (I have deleted the TER
this way
pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep
interactive
and selected y.
Then everything is OK in mdrun step.
I don't know what the different in -chainsep interactive and -chainsep ter is
in my case.
They seems to the same in my two chain system.
otunf.html
But it also useless to me.
And in my mdp I use thermostat and barostat, which means my system is NPT.
Does anything wrong in my methods?
Sincerely yours,
Hsin-Lin
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the other 2ns for 400K only, then
the protein is still stable and the value is almost the same in radius of
gyration.
Below is the mdp file of the heating.
What's wrong with my system?
regards,
Hsin-Lin
-
title = ttt
cpp
= /lib/cpp
constr
ause mdrun -nc is faster the mdrun_mpi.
/>/ That make me confused.
/>/ Am I right to use mdrun -nc to run parallel job in this way?
/
For a single, multi-core workstation, mdrun -nt is correct.
Thank you for you answer, then I can feel easy in mind to use this argument,
-nt.
And also thanks
the same as which is employed by mdrun_mpi?
(Exactly I never use mdrun_mpi more than one machine since the ethernet
between machines is very slow here.)
If mdrun -nc is available.
Do we have another commend support CPUs more than one in the same machine.
Sincerely yours,
Hsin-Lin
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Hi,
Thank you.
I use gcc v4.4 and complete the installing.
Sincerely yours,
Hsin-Lin
> Hi,
>
> That compiler is ancient (thought it might have SSE2 support) as well
> as the OS, I guess (RHEL 3?). Still, the CPU does support SSE2 so if
> you can get a gcc 4.1 or later on it y
.@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Hsin-Lin Chiang wrote:
> > Hi,
> >
> > Thank you for your reply.
> > I'm not so good in computer.
> > I think the platform you ask me is "Linux", and kernel is
Hi,
Thank you for your reply.
I'm not so good in computer.
I think the platform you ask me is "Linux", and kernel is 2.4.21-60.ELsmp
The compiler is gcc v3.2.3 in the machine in my institute.
Sincerely yours,
Hsin-Lin
> Message: 1
> Date: Thu, 26 May 2011 18:03:09 +0200
Hi,
I met some problem on installing gromacs 4.5.4
Below is the log.
I'm soory I can't distinguish the important part and I post all of them.
I'll appreciate for any help.
Hsin-Lin
-
Making all in include
make[1]: Entering directory `/stathome/jiangsl/src/gromac
much longer trajectories should show mutual convergence, and the movie is not
> a reasonable way to look for it.
>
> Mark
Sorry I don't understand you here.
Do you mean second way seems to more correct?
And what kind of mutual convergence you mean here?
Does It mean I can try to f
rgy within protein also fluctuate in an unstable way.
On the contrary, the second method generate a stable movie and fluctuation of
interaction energy.
Theotically these two should be the same, right?
Is anything wrong in my work?
Sincerely yours,
Hsin-Lin
--- End of Forward
generate a stable movie and fluctuation of
interaction energy.
Theotically these two should be the same, right?
Is anything wrong in my work?
Sincerely yours,
Hsin-Lin
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right?
Is anything wrong in my work?
Sincerely yours,
Hsin-Lin
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Hi, Mark,
I'll adopt your suggestion.
Thank you for your reply again.
Sincerely yours,
Hsin-Lin
On 7/12/2010 6:01 PM, Hsin-Lin Chiang wrote:
>/
/>>/ Ah, sorry, I didn't read you well enough.
/>>/
/>>/ I've just seen that GROMACS 4.5 introduced trjconv
think I can use -sep and write a shell script to combine frames together.
Sincerely yours,
Hsin-Lin
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ltaneously).
Would you please teach how to use -skip -sep to get the same kind of
file which include all of 1000ps time frames together in a 1ns gro file?
I'll appreciate to any helps.
Sincerely yours,
Hsin-Lin
>/Hi,
/>/
/>/ My time unit is 1ps and today I have 300ns da
6,
2000.00012, 3000.00024, and t= 4000.00024.
I know I can add -timestep 1 to solve this problem and let file can be
truncated at t= 1000.6.
How does this kind of inaccurate time frames happen?
Is this trajectory a wrong result?
Sincerely yours,
Hsin-Lin
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Hi, Mark
So, You mean I can get correct extending simulation without using -e ede
and -t trr in GROMACS ver.4.
Then I can set my mind at rest.
Thank you for your reply.
Hsin-Lin
Hi,
Today I use serach and find this topic.
I got confused.
http://www.gromacs.org/Documentation/How-tos
ACS version is 4.0.5.
Am I right to use lines above to do extending simulation?
Hsin-Lin
>
>
> - Original Message -
> From: Yongchul Chung
> Date: Thursday, November 4, 2010 10:28
> Subject: [gmx-users] extending simulation without cpt file
> To: Discussion lis
umber of H-bonds in my
last message.
So I think maybe it's just because the manners of two programs are
different.
regards,
Hsin-Lin
> Hsin-Lin Chiang skrev:
>> Hi,
>>
>> I use g_hbond to analyze the system with two peptide.
>> And I introduce the nd
omted.
How should I do to exclude the intra-H-bond on one peptide?
Hsin-Lin
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Hi ,Mark:
I had announced that my system is a dimer with each peptides have 6
residues in my first post.
I'm sorry if I didn't express it to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a dimer?
regards,
Hsin-Lin
Hi, Justin:
I post my
Hi ,Mark:
I had announced my system is a dimer with each peptides have 6 residues.
I'm sorry if I didn't express it to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a dimer?
regards,
Hsin-Lin
Hi, Justin:
I post my coordinate with protein
Hi, Justin:
I post my coordinate with protein translated by trjconv
By this gro file, I get 0 structure and 13 coils.
regards,
Hsin-Lin
Generated by trjconv : Protein in water t= 0.0
144
1LEU N1 2.499 1.707 2.735 -0.1664 0.1749 0.5034
1LEU H12 2.496
Hi, Justin
Thank you for your patience.
According your reply, I used trjconv to write only protein group into
another file.
I execute do_dssp again in group "protein"and "mainchain" respectively but
still get coils more than total residues.
Why?
Hsin-Lin
Hsin-Lin
.org/wiki/DSSP_%28protein%29
the hydrogen bonds are dicided by O, C, H, and N four atoms.
How can we get dssp analysis by backbone that includes only NCCNCCNCC.....?
Sincerely yours,
Hsin-Lin
> Hsin-Lin wrote:
> > Hi,
> >
> > I use do_dssp to generate xvg file collect the last li
ach peptide has 6 residue.
And the number I choose to analyze is "1. Protein".
Now I have a question, if I want to calculate the percentage of secondary
structure.
In the example above, is it calculated in this way 5/12=42%?
Hsin-Lin
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h
n our lab. is
too slow to do parallel simulation.
What the effect should be in this kind of slow Ethernet environment?
Is it why the utility of CPU are always less than 35% when I submit the same
job to the machine in our lab.?
Hsin-Lin
> Hi,
>
> I want to use my dual core PC to do
greatly appreciated.
Hsin-Lin
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my analysis I only need xvg file.
How can I do to get xvg output without the others accompanied?
Hsin-Lin
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Please don&#
s assigned to mehave been 100%
loading,
and the CPU source availble to me is less then 10%.
I think there is something wrong with my submit script or executable script,
and I post them in my previous message.
How should I correct my script?
Hsin-Lin
> Hi,
>
> how many CPUs do you
ssigned to mehave been 100%
loading,
and the CPU source availble to me is less then 10%.
I think there is something wrong with my submit script or executable script,
so I post them in my question before.(please see those below)
Hsin-Lin
> Hi,
>
> how many CPUs do you try to use? How
00ns.edr \
-o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \
-g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \
-c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro
-
Hsin-Lin
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