Justin
I have one extra question about parametrisation of the bond type
Initially I had -c-c- bond so both atoms were in the sp3 hybridization.
I've changed bond type between that atoms to the gb_16 ( from phe ring) to
define them as the c=c but during the simulation I've noticed that the
bond
Hi Mark! Thanks for the response.
Just to follow up, the problem was that another program was deleting md.log before it could be accessed. This is entirely not the fault of GROMACS, however a more descriptive error message could have saved us some time (e.g. "md.log not found" as
On Sat, 2012-06-09 at 15:33 -0700, Mr Bernard Ramos wrote:
Hi everyone!
I have a 20 ns simulation (2fs timestep but coordinates saved every
0.2 ps) and I was able to calculate the mean-square-displacement of
the oxygen atoms of my water solvent. The entire MSD plot looks very
linear to
On 6/10/12 3:06 AM, James Starlight wrote:
Justin
I have one extra question about parametrisation of the bond type
Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've
changed bond type between that atoms to the gb_16 ( from phe ring) to define
them as the c=c but
Dear gmx users,
If i want to simulate the system in Temperature=323 k , am I supposed to change
the ref-t or gen-t in NVT file?
Thanks in advance
Sincerely,
Shima--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive
On 6/10/12 7:46 AM, Shima Arasteh wrote:
Dear gmx users,
If i want to simulate the system in Temperature=323 k , am I supposed to change
the ref-t or gen-t in NVT file?
Both. The gen_temp parameter generates the velocities according to a Maxwell
distribution. The ref_t parameter is what
Justin,
thanks again for help.
Finally is there any generall solution to parametrise hetero-groups
covalently bonded with the protein ? Many proteins consist of such groups
e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic
groups in the enzymes.
I've tried to make
On 6/10/12 8:03 AM, James Starlight wrote:
Justin,
thanks again for help.
Finally is there any generall solution to parametrise hetero-groups covalently
bonded with the protein ? Many proteins consist of such groups e.g chromophore
in GFP, retinall in rhodopsin as well as some prostetic
I was performing protein simulation. For capping I added ACE and NH2
residues to my pdb file. I was using charmm force field , so i made changes
to the rtp entry in charmm aminoacids.rtp.
siddhant@ubuntu:~/sura$ pdb2gmx -f bestins.pdb -o first.gro -ter
:-) G R O M A
On 6/10/12 8:19 AM, siddhant jain wrote:
I was performing protein simulation. For capping I added ACE and NH2 residues to
my pdb file. I was using charmm force field , so i made changes to the rtp entry
in charmm aminoacids.rtp.
siddhant@ubuntu:~/sura$ pdb2gmx -f bestins.pdb -o first.gro
Greetings,
This might end up being a silly/embarrassing question, and if so, I
apologize. I feel like I may be making a conceptual mistake, but I'm not
sure.
Is it true that a hydrogen bond is of the following form?
Donor---Hydrogen ... Acceptor
Is this the correct order? I think so. For
On 6/10/12 10:36 AM, Andrew DeYoung wrote:
Greetings,
This might end up being a silly/embarrassing question, and if so, I
apologize. I feel like I may be making a conceptual mistake, but I'm not
sure.
Is it true that a hydrogen bond is of the following form?
Donor---Hydrogen ... Acceptor
Hi
Is it possible to convert a .pdb file to a .xyz file with GROMACS?
At this point there shouldn't be a force field or final topology, I just want
to convert this formats to each other. Is it possible with GROMACS?
Greetings
Lara
--
gmx-users mailing listgmx-users@gromacs.org
Hi,
If I understand correctly, currently the Gromacs GPU acceleration does
not support energy minimization. Is this so? Are there any plans to
include it in the 4.6 version or in a later one (i.e. to allow, say,
integrator = steep or cg in mdrun-gpu)? I would find such options
extremely useful.
Thanks for your reply.
So if I have to simulate the system at T=323 K , I need to set both ref-temp
and gen-temp at 323K. Right? I guess no difference between two items , I mean
ref and gen, to be set at what temperature!
Sincerely,
Shima
From: Justin A.
Why do you want to use Gromacs?
I would suggest to use openBabel, which can convert a whole bunch of
file formats...
Regards,
Matthias
Am 10.06.2012 16:55, schrieb Lara Bunte:
Hi
Is it possible to convert a .pdb file to a .xyz file with GROMACS?
At this point there shouldn't be a force
Thanks for mentioning my errors. I have corrected them. But now the problem
is there is no rtp entry for NH2 in charmm. Here is what happens now-
Using the Charmm27 force field in directory charmm27.ff
pdb2gmx -f bestins.pdb -o first.gro -ter
*entering 8 for charmm 27 force field*
Opening
On 6/10/12 3:14 PM, siddhant jain wrote:
Thanks for mentioning my errors. I have corrected them. But now the problem is
there is no rtp entry for NH2 in charmm. Here is what happens now-
If you want NH2 as a cap, you will need to come up with parameters for it. An
alternative is NAC. See
Use editconf http://manual.gromacs.org/current/online/editconf.html
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sun, Jun 10, 2012 at 11:30 PM, Matthias Ernst
matthias.ern...@student.kit.edu wrote:
Why do you want to use Gromacs?
I would suggest to use openBabel, which can convert
On Fri, Jun 8, 2012 at 12:21 PM, Wang, Yuhang ywang...@illinois.edu wrote:
Dear Gromacs developers,
I have benchmarked the desolvation free energy calculation of Na+ ion
using Gromacs and NAMD (for comparison). There is a large difference in the
electrostatic desolvation free energy (see
Dear Gromacs users
I have a question abut radius of gyration in proteins. I want to calculate it
via MD simulation for calcium pump protein. Following the same method as
described in justin lezozyme tutorial, we have dissolved the protein in water.
I want to know that is it wise to study this
Hello
I want to make sure about the command that I use. I have MD result for protein
simulation MD for 1 ns. I want to continue this simulation for longer time.
Check point file should be used for continuation:
grompp -f md.mdp -c md-out.gro -t md.cpt -p topol.top -o md_2.tpr
** md-out.gro is
Dear Gromacs users
I have checked something today and it seems starnge to me. Doing the Justin
lyzozyme tutorial, I checked the performance of our parallel system.
Subimitting the job on 8 processors of one node, I get0.86 ns/daywhich seems to
be very weak performance. Do you have any idea
Hi,
if you want to continue the simulation, you'd better use tpbconv command to
generate a new *.tpr, or if you are using grompp command you have also to have
-c previouse.tpr in the command line, there is no need for *.gro or *.top.
From: delara aghaie
On 11/06/2012 3:06 PM, delara aghaie wrote:
Dear Gromacs users
I have checked something today and it seems starnge to me. Doing the
Justin lyzozyme tutorial, I checked the performance of our parallel
system. Subimitting the job on 8 processors of one node, I get0.86
ns/daywhich seems to be
On 11/06/2012 2:43 PM, delara aghaie wrote:
Hello
I want to make sure about the command that I use. I have MD result for
protein simulation MD for 1 ns. I want to continue this simulation for
longer time. Check point file should be used for continuation:
grompp -f md.mdp -c md-out.gro -t
On 11/06/2012 2:32 AM, ifat shub wrote:
Hi,
If I understand correctly, currently the Gromacs GPU acceleration does
not support energy minimization. Is this so? Are there any plans to
include it in the 4.6 version or in a later one (i.e. to allow, say,
integrator = steep or cg in mdrun-gpu)? I
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