For example;
grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr
mdrun -v -deffnm run
...
1500 steps, 3.0 ps.
step 100, will finish Sun Nov 27 19:11:00 2011
Sometimes it shows as the following:
1500 steps, 3.0 ps.
That is, there is not will finish Sun Nov 27
On 19/10/2011 5:04 PM, ahmet y?ld?r?m wrote:
For example;
grompp -f run.mdp -p topol.top -c pr.gro -n index.ndx -o run.tpr
mdrun -v -deffnm run
...
1500 steps, 3.0 ps.
step 100, will finish Sun Nov 27 19:11:00 2011
Sometimes it shows as the following:
1500 steps, 3.0 ps.
Thanks for your reply
I dont understand step number is at least as large as nstlist. can you
some explain?
Furthermore, if the file system doesnt write the buffer to the destination
screen/file, then does that mean there is a problem? for example
if it shows as the following:
1500 steps,
On 19/10/2011 5:25 PM, ahmet y?ld?r?m wrote:
Thanks for your reply
I dont understand step number is at least as large as nstlist. can
you some explain?
The first output you cite was written at step 100, of the 15M you asked
for. nstlist is in your .mdp file. All this stuff really doesn't
Justin, hello!
Today I've done 1ns npt equilibtation of my system
this is the final result of this stage of simulation
http://www.sendspace.com/file/nw032q
So I wounder to discuss some notes with imerged during the simulation
1- As you see some water molecules have moved into membrane during
Hi Justin!
Do you maybe have an example of such a protein (preferably not too large :-),
that I could run some tests on?
I'd be interested in seeing if there has been any bugs introduced in the cutoff
code that destabilises proteins that way.
Thanks
/Per
18 okt 2011 kl. 23:41 skrev Justin A.
Thomas, Justin thank you for that information
Recently I've alredy tried to investigate CHARMM36 ff. I found that
lipid.rtp of that ff consist of data for different DPP lipids. But in those
DPPC lipid bilayer that I've used in the Justin's tutorial consist of 50
atoms for each monomer. In
Hi all.
I want to ask you a question about the length of dynamics. Is it enough to
set time at 3-5ns to see the motion and affinity of the ligand (nucleotide
derivate) the protein's domain size is nearly 200 aminoacids. The protein
was optimized earlier. Moreover, is it enough for drug design
Hi,
I am doing Essential Dynamics on a protein (150 residues). The simulation is
100ns long and the RMSD becomes very stable after 25ns.
I have gone through the mailing list archives but could not find a precise
answer to the following question.
When I calculate the cosine content for the first
Dear gromacs users,
I am inspecting the charmm27.ff/ions.itp file and I noticed that the ZN ion
has a negative charge:
[ moleculetype ]
; molname nrexcl
ZN 1
[ atoms ]
; idat type res nr residu name at name cg nr charge
1 ZN 1 ZN ZN 1
Dear Gromacs users,
I have a problem in simulating microtubule hetero-dimer. I was trying to
include K+ and CL- ions to counter balance as well as to maintain the
desired concn (intra cellular concentration of KCl is approx 140mM) using
the command
genion -s ions.tpr -o solv_ions.gro -p topol.top
Dear Itamar and Justin,
Thank you for your responses. I will make the changes to the mdp files and
see how easy or hard it is to make the shift from 4.0.5 to 4.5.
Sincerely,
Sapna
On Tue, Oct 18, 2011 at 10:28 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Itamar Kass wrote:
Hi Sapna,
It
Dear all,
I want to double check, the output from an REMD simulation with Gromacs is the
trajectory at constant Temp and whe you demux it with demux.pl, this is the
trajectory of the replica which starts at a given tempurature and how it
evolves through time?
For instance, if _0.tpr file
On 19/10/2011 9:55 PM, Wright, Louise wrote:
Dear all,
I want to double check, the output from an REMD simulation with
Gromacs is the trajectory at constant Temp and whe you demux it with
demux.pl, this is the trajectory of the replica which starts at a
given tempurature and how it evolves
On 19/10/2011 9:43 PM, Venkat Reddy wrote:
Dear Gromacs users,
I have a problem in simulating microtubule hetero-dimer. I was trying
to include K+ and CL- ions to counter balance as well as to maintain
the desired concn (intra cellular concentration of KCl is approx
140mM) using the command
Hi Vivek,
I explained related matters in some detail on this list earlier, and
would urge not to use a structure other than the average for
determining the components.
The results on the cosine contents can be illustrated as follows:
I. Using average
Imagine you're moving from place A to place
francesco oteri wrote:
Dear gromacs users,
I am inspecting the charmm27.ff/ions.itp file and I noticed that the ZN
ion has a negative charge:
[ moleculetype ]
; molname nrexcl
ZN 1
[ atoms ]
; idat type res nr residu name at name cg nr charge
1 ZN 1
On 19/10/2011 9:12 PM, francesco oteri wrote:
Dear gromacs users,
I am inspecting the charmm27.ff/ions.itp file and I noticed that the
ZN ion has a negative charge:
[ moleculetype ]
; molname nrexcl
ZN 1
[ atoms ]
; idat type res nr residu name at name cg nr charge
1
James Starlight wrote:
Justin, hello!
Today I've done 1ns npt equilibtation of my system
this is the final result of this stage of simulation
http://www.sendspace.com/file/nw032q
As I said before, I cannot obtain files from this site.
So I wounder to discuss some notes with imerged
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't get
any error while performing the minimization but when visualised the pdb file
after the minimization the chains of the protein complex separated.
What could be the reason.
Thanks,
Aiswarya
Sent from my
Dear GMX-users,
I found a question in 2009 asking which format of improper does
OPLS dihedral gromacs use. I have the same question, is it periodic or
harmonic?
If it is periodic, why in its ffbonded.itp file: #define improper_O_C_X_Y
180.0 43.93200 2 what do they mean?
Also, when I plug in
1 check with the rtp files in your forcefield, especially the parameters
2 check with the imput pdb file, the format matters a lot.
On Wed, Oct 19, 2011 at 8:18 AM, aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't
get any
aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't get
any error while performing the minimization but when visualised the pdb file
after the minimization the chains of the protein complex separated.
What could be the reason.
Justin,
As I said before, I cannot obtain files from this site.
Could you provide me with the fileshare server wich you have access? I cant
uploat files to that mail list indirectly due to the limitation of the size
for attached files
If water is leaking into your membrane, you may
James Starlight wrote:
Justin,
As I said before, I cannot obtain files from this site.
Could you provide me with the fileshare server wich you have access? I
cant uploat files to that mail list indirectly due to the limitation of
the size for attached files
I don't need the
On 20/10/2011 12:26 AM, mu xiaojia wrote:
Dear GMX-users,
I found a question in 2009 asking which format of improper does
OPLS dihedral gromacs use. I have the same question, is it periodic or
harmonic?
The quote below clearly says they are implemented as proper periodic
dihedrals.
If it
Dear Jia,
I found a question in 2009 asking which format of improper does
OPLS dihedral gromacs use. I have the same question, is it periodic or
harmonic? If it is periodic, why in its ffbonded.itp file: #define
improper_O_C_X_Y 180.0 43.93200 2 what do they mean?
this means that the dihedral
Justin,
I don't need the files. I'm just trying to save you time. If I want to see
a coordinate file, I'll ask for it to be sent to me directly. I have seen
no such need yet.
Ok.
Application of pressure causes the box to change. The water won't leak in
during NVT because the
James Starlight wrote:
Justin,
I don't need the files. I'm just trying to save you time. If I
want to see a coordinate file, I'll ask for it to be sent to me
directly. I have seen no such need yet.
Ok.
Application of pressure causes the box to change. The water
Hi Justin,
I used the below g_select command to get the list of phosphorus atoms (from
DPPC lipid) within 0.5 nm of protein.
g_select -f ordered.xtc -n initial.ndx -on select.ndx -select name P and
within 0.5 of group Protein -s md_500ns.tpr -b 10 -dt 1000
My output is an index file
Poojari, Chetan wrote:
Hi Justin,
I used the below g_select command to get the list of phosphorus atoms (from DPPC lipid) within 0.5 nm of protein.
g_select -f ordered.xtc -n initial.ndx -on select.ndx -select name P and within 0.5
of group Protein -s md_500ns.tpr -b 10 -dt 1000
My
Hello GROMACS users,
I wish to simulate an alkanethiol self-assembled monolayer on a gold
surface. The first molecule I am attempting to model is quite simple:
CH3(CH2)11S. I have constructed a united atom force field based on
parameters published by Hautman and Klein (J. Chem. Phys. 1989) to
Hello,
I did change nsttcouple and nstpcouple but the simulations that run in 4.0.5
are still crashing in 4.5.4. I think it is related to constraints but I am
unable to figure out exactly what is different. I have pasted both my
topology and mdp (updated for 4.5.4) files. Any ideas? I have read
Olivia Waring wrote:
Hello GROMACS users,
I wish to simulate an alkanethiol self-assembled monolayer on a gold
surface. The first molecule I am attempting to model is quite simple:
CH3(CH2)11S. I have constructed a united atom force field based on
parameters published by Hautman and Klein
Hi Sopna,
First, can you attached the crash report of GROMACS 4.5, so we can have a look
on it? Second, are you doing EM and PR before you run it using 4.5? Even if you
transfer a stable system from 4.0 it might need some equilibration before you
actually run MD, specifically if you assign new
On 20/10/2011 8:40 AM, Sapna Sarupria wrote:
Hello,
I did change nsttcouple and nstpcouple but the simulations that run in
4.0.5 are still crashing in 4.5.4. I think it is related to
constraints but I am unable to figure out exactly what is different. I
have pasted both my topology and mdp
Hi Itamar and Mark,
The error message is pasted below. I tried both running minimization and
then running the MD; and using a configuration from a previous simulation
(that was run using Gromacs 4.0.5). In both these case the simulations are
crashing. The error message is similar.
Mark, Yes
Hi,
All the parameters are ok, still i get the complex separated.
On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya.pa...@gmail.com wrote:
Hi Users,
I performed a simple minimization for a protein complex in vacuum. Didn't
get any error while performing
On 20/10/2011 4:14 PM, aiswarya pawar wrote:
Hi,
All the parameters are ok, still i get the complex separated.
Simulation parameters have nothing to do with the phenomena in the FAQ
Justin pointed out to you. Please read it.
Mark
On Wed, Oct 19, 2011 at 7:02 PM, Justin A. Lemkul
Hi,
It is not clear what are the units of SAS from g_SAS. The output gives
the units - xaxis label Time (ps)
@yaxis label Area (nm\S2\N).
I would really appreciate it if someone could elaborate on (nm/S2/N).
Thanks and regards,
Pooja
--
Quaerendo Invenietis-Seek and you shall
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