Dear GROMACS Experts,
I am using GROMACS to simulate the self-diffusion coefficient of a wide
range of pure systems (e.g. alkanes).
Unfortunately the information given in the manual regarding g_msd and its
exact calculation in GROMACS is insufficient for me.
Does somebody got some idea of
Dear users,
Am I clear with the question?
Thank you
Kavya
On Wed, Dec 12, 2012 at 1:36 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was calculating solvent accessible surface area for a trajectory
using g_sas. I used an index file with 3 sets (A, B, C) of mutually
exclusive
What are the possible solutions to solve the problem?
My system is composed of protein, POPC, ions, and water. I follow the
approached suggested in kalp15-DPPC tutorial.
And I got such an incorrect potential for the first grompp.
Would you please guide me?
I would appreciate ur suggestions.
Also I've made the same parameters with the capped chromophore (NH2 on
the C-term (instead of OH) and ACE on the N term (instead of H).
When I've defined that chromophore as the Protein I've obtained an error
Fatal error:
Atom OXT in residue CRO 66 was not found in rtp entry CRO with 38 atoms
What are the possible solutions to solve the problem?
My system is composed of protein, POPC, ions, and water. I follow the
approached suggested in kalp15-DPPC tutorial.
And I got such an incorrect potential for the first grompp.
Would you please guide me?
I would appreciate ur suggestions.
Dear users,
Anything wrong in my question?
Kindly give some suggestions.
Thank you
Kavya
On Wed, Dec 12, 2012 at 3:23 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Am I clear with the question?
Thank you
Kavya
On Wed, Dec 12, 2012 at 1:36 PM, Kavyashree M hmkv...@gmail.com
You can just turn the power off :-) The checkpointing mechanism ensures you
already have all your output up to the time of the last checkpoint (default
every 15 minutes). You can use gmxcheck on these files during the
simulation to see what's in them.
Mark
On Wed, Dec 12, 2012 at 10:26 AM, Ali
thanks for the reply.
How i can check the stability of integration?
If i consider 2 first ns for equlibration, can I trust the rest results?
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Tuesday, December
On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was calculating solvent accessible surface area for a trajectory
using g_sas. I used an index file with 3 sets (A, B, C) of mutually
exclusive residues but summing up to 20 amino acids. Then using
g_sas
Hi Kavya,
Can you better describe your system?
As Mark suggested, could you supply some number?
Francesco
2012/12/12 Mark Abraham mark.j.abra...@gmail.com
On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was calculating solvent accessible surface
Oh that problem was imperically resolved by renamind O2 ( which are
not terminal but pdb2gmx define them as a terminal ) atom to O3
The only question about my chromophore is the definition of the IMPROPER groups.
As I've posted above my initial model was CAPPED from C and N termi by
NH2 and Ace.
How about it that I get a positive potential energy for a system of only
protein and POPC? Makes sense?
Thanks for your explanation.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
On 12/12/12 5:16 AM, Shima Arasteh wrote:
What are the possible solutions to solve the problem?
My system is composed of protein, POPC, ions, and water. I follow the
approached suggested in kalp15-DPPC tutorial.
And I got such an incorrect potential for the first grompp.
Would you please
On 12/12/12 4:37 AM, dakoenig wrote:
Dear GROMACS Experts,
I am using GROMACS to simulate the self-diffusion coefficient of a wide
range of pure systems (e.g. alkanes).
Unfortunately the information given in the manual regarding g_msd and its
exact calculation in GROMACS is insufficient for
On 12/12/12 12:37 AM, James Starlight wrote:
That the mollecule that I made
[ CRO ]
[ atoms ]
CG2 CB 0.0284 0
CD1 CB -0.1500 1
CD2 CB -0.1500 2
CE1 CB -0.1500 3
CE2 CB -0.1500 4
CZCB 0.0825 5
HLH 0.3600 39
NRNH1-0.9900 6
CA1 CR
On 12/12/12 6:10 AM, Bahar Mehrpuyan wrote:
thanks for the reply.
How i can check the stability of integration?
If the integration is unstable, the system will crash.
If i consider 2 first ns for equlibration, can I trust the rest results?
Without significantly more information, no one
On 12/12/12 6:54 AM, James Starlight wrote:
Oh that problem was imperically resolved by renamind O2 ( which are
not terminal but pdb2gmx define them as a terminal ) atom to O3
The only question about my chromophore is the definition of the IMPROPER groups.
As I've posted above my initial
I write the exact commands up to grompp here, not to miss anything;
1. pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
2. grompp -f minim.mdp -c md-popc.gro -p topol_popc.top -o em.tpr
3. trjconv -s em.tpr -f md-popc.gro -o popc-whole.gro -pbc mol -ur compact
4. editconf
On 12/12/12 8:14 AM, Shima Arasteh wrote:
I write the exact commands up to grompp here, not to miss anything;
1. pdb2gmx -f dimer-rotated.pdb -o dimer-processed.pdb -ter -water tip3p
2. grompp -f minim.mdp -c md-popc.gro -p topol_popc.top -o em.tpr
3. trjconv -s em.tpr -f md-popc.gro -o
Hi Bipin Singh,
the parameters -deltaF0, -deltaF, -tau, -alpha, and -T are used only
for flooding and have no effect in pure essential dynamics. Which coordinates
appear in the output trajectory (*.trr, *.xtc) is exclusively controlled
by .mdp options (i.e. the group you select there), not by the
Thank you all!
On Tue, Dec 11, 2012 at 12:54 PM, Leandro Bortot leandro@gmail.com wrote:
I have made SMD simulations in order to separate a Ca2+ ion from its
complexation site in the protein, which had charge of about -6 e. Without
position constraints in the protein alpha carbons it
Thank you very much for your replies.
The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.
The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R
So these are set in an index file and i used each one of these
to calculate sasa in
Justin,
The IMPROPERS consisted of atom names (its correct as I understood).
The bond tern I've changed. The resulted RTP
[CRO]
[ atoms ]
CG2 CB 0.0284 0
CD1 CB-0.1500 1
CD2 CB-0.1500 2
CE1 CB-0.1500 3
CE2 CB-0.1500 4
CZ CB 0.0825 5
NNC=O -0.7301 6
CA1 CR
On 12/12/12 9:37 AM, Kavyashree M wrote:
Thank you very much for your replies.
The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.
The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R
So these are set in an index file and i
Sir,
Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.
Kavya
On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/12/12 9:37 AM, Kavyashree M wrote:
Thank you very
I meant subset :)
On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M hmkv...@gmail.com wrote:
Sir,
Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.
Kavya
On Wed, Dec 12, 2012 at 8:16 PM,
Unix signals SIGTERM and SIGUSR1 can be sent to mdrun that will cause it to
stop next step or next neighbour search step. That ensures an orderly
termination, inasmuch as the file system buffering then has time to flush
before the power goes off :-) Various shell or queue system commands can
send
New problem during processing of y structure via GROMPP
ERROR 217 [file topol.top, line 34183]:
No default Improper Dih. types
ERROR 218 [file topol.top, line 34184]:
No default Improper Dih. types
ERROR 219 [file topol.top, line 34185]:
No default Improper Dih. types
ERROR 220 [file
Hi,
You can use VMD for drawing graphene and carbon nanotube.
Best Regards,
On Mon, Dec 10, 2012 at 1:44 AM, Amir Abbasi amir.abbas...@yahoo.comwrote:
Hi,
I know that here for discussion about Gromacs,but I want to ask which
program is the best for structure building and manipulating. I work
On 12/12/12 11:49 AM, James Starlight wrote:
New problem during processing of y structure via GROMPP
ERROR 217 [file topol.top, line 34183]:
No default Improper Dih. types
ERROR 218 [file topol.top, line 34184]:
No default Improper Dih. types
ERROR 219 [file topol.top, line 34185]:
Justin,
That errors was strange to me because I've already used Swiss's ITP
files for diffusional ligands including them in the topol.top of my
protein and there were no such errors about non-standart types in any
terms. It seems that some additions to the ffbonded.itp also required
besides the
Thanks, couldn't see the wood for the trees. Clear as daylight now.
On 11/12/12 19:39, Mark Abraham wrote:
Yes. Read about analysis groups in chapter 8.
Mark
On Tue, Dec 11, 2012 at 8:20 PM, khuws kh...@khuws.plus.com wrote:
Thanks,
I forgot to mention that I need the force
On 12/12/12 3:11 PM, James Starlight wrote:
Justin,
That errors was strange to me because I've already used Swiss's ITP
files for diffusional ligands including them in the topol.top of my
protein and there were no such errors about non-standart types in any
terms. It seems that some additions
We specialise in building trees, unfortunately :)
On Wed, Dec 12, 2012 at 9:04 PM, Keith kh...@khuws.plus.com wrote:
Thanks, couldn't see the wood for the trees. Clear as daylight now.
On 11/12/12 19:39, Mark Abraham wrote:
Yes. Read about analysis groups in chapter 8.
Mark
On Tue,
Dear Justin,
Thank you for your reply. To be sure I carefully ran the simulations again
using the following .mdp file that includes the pull lines and
-DPOSRES_B to restrain chain B from being pulled when chain A is being
pulled (it is the .mdp file given in the tutorial):
title =
On 12/12/12 5:15 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. To be sure I carefully ran the simulations again
using the following .mdp file that includes the pull lines and
-DPOSRES_B to restrain chain B from being pulled when chain A is being
pulled (it is the .mdp
On 12/12/12 5:26 PM, Justin Lemkul wrote:
On 12/12/12 5:15 PM, Davide Mercadante wrote:
Dear Justin,
Thank you for your reply. To be sure I carefully ran the simulations again
using the following .mdp file that includes the pull lines and
-DPOSRES_B to restrain chain B from being pulled
Dear gmx-users：
I want to analysis PCA for many crystal strcutures, comparing with MD
trajectories, but how to build xtc file from many same structures whchi are
different conforamtional states.
thank you
best regards!
--
gmx-users mailing listgmx-users@gromacs.org
On 12/12/12 9:29 PM, xi zhao wrote:
Dear gmx-users：
I want to analysis PCA for many crystal strcutures, comparing with MD
trajectories, but how to build xtc file from many same structures whchi are
different conforamtional states.
Each configuration can be converted to an .xtc frame
Dear users,
I have used grompp command for minimising my protein and ligand in membrane
after using inflategro command.
My system has no problem in visualizing in VMD. The protein is in proper
order
But I am getting the error
---
Program grompp,
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