Hello,
I am interested in dynamical analysis of my protein. In the manual, it says
-ascii generates a file that includes the whole covariance matrix, and -xpma
writes the atomic covariance matrix per pair of atoms. I was wondering if
there is a way to have this atomic covariaces in the .dat file wi
Hello,
I am simulating a protein using side chain pKa values estimated from
PROPKA based on crystal structure of the protein. I re-estimated the pKa
of side chains after running 10 independent replica of 50ns (500ns in
total) of NPT simulations. It turned out that the average pKa of a
surface Glu w
t,
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-08-13 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
On 1/8/13 8:05 PM, Payman Pirz
:25 PM, Payman Pirzadeh wrote:
> I had modified three files: aminoacids.rtp, aminoacids.hdb and
> residuetypes.dat. All these modifications were done prior running pdb2gmx.
> So, I will be glad if you could let me know what the problem is.
From that description, everything should be fine.
-boun...@gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-08-13 5:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
On 1/8/13 6:58 PM, Payman Pirzadeh wrote:
> Hi,
> Found my solution; made an index file which had the prote
: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
On 1/8/13 6:09 PM, Payman Pirzadeh wrote:
> Dear Justin,
> Thanks for the tips. Things worked smoothly up to the point when I
> wanted to run an actual simulation. When I wanted to run gro
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin Lemkul
Sent: January-08-13 4:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
On 1/8/13 6:09 PM, Payman Pirzadeh wrote:
> Dear Justin,
> Thanks for the tips. Things worked sm
ng pdb2gmx
On 1/8/13 1:37 AM, Payman Pirzadeh wrote:
> Dear Justin,
> Thanks for your suggestions. It all made sense.
> But I ran into a strange problem. I checked the mail list, and all I
> found was about misspelling the force field name. I copied the whole
> gromos53a5.ff directo
ary-07-13 5:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
On 1/7/13 7:36 PM, Payman Pirzadeh wrote:
> Two clarifications:
> 1. can utilization of an index file help during topology generation
> for my problem?
No. Reading pdb2gm
...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: January-07-13 5:28 PM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] selecting res CYS from G53a5 using pdb2gmx
Dear Justin,
I have been able to temporarily solve my force field parameter problem (at
least test the new para
53a5 using pdb2gmx
On 1/6/13 4:45 PM, Payman Pirzadeh wrote:
> Hi,
> I am using gromacs 4.5.4, and I am generating a topology file using
> G53a5 force field. My protein has a Cys residue which is supposed to
> be in thiolate state (negatively charged side chain). During issuing
&
Hi,
I am using gromacs 4.5.4, and I am generating a topology file using G53a5
force field. My protein has a Cys residue which is supposed to be in
thiolate state (negatively charged side chain). During issuing the pdb2gmx
command I use the switch -inter to be prompted about the charge state of the
Hello,
I am trying to generate a topology file for my protein which has three
disulfide bonds using ffG53a5. I realized in the topology file that the
force field parameters for bonds, angle and dihedrals of my S-S bonds are
missing. I found the following thread about this issue:
http://lists.grom
Hello,
In calculation of the surf*surftension with g_energy, does this quantity
have any meaning when one deals with a protein in water(water fills up the
box)? Can it be indicative of the surface tension of protein and water?
Thanks.
Paymon
--
gmx-users mailing listgmx-users@gromacs.org
ht
Hello,
I am using gromacs 4.5.4. In g_energy I see an option about #surf*surfTen.
Could you please clarify how it is calculated? In a system with a protein
and water, what does it correspond to?
Best,
Paymon
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...
...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: February-13-12 12:24 AM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] g_rdf -surf
Hello,
Thanks for your attention. A word was missing in my previous e-mail!! The
g(r) is NOT normalized.
Here was my command:
12 5:54 PM, Payman Pirzadeh wrote:
Hello,
I am trying to calculate the RDF of water next to surface of certain
residues. I used the an index file which includes the residues as the first
group, and the #12 option (SOL) in the g_rdf, and used the option '-surf
res' on the prompt.
Ple
Hello,
I am trying to calculate the RDF of water next to surface of certain
residues. I used the an index file which includes the residues as the first
group, and the #12 option (SOL) in the g_rdf, and used the option '-surf
res' on the prompt. However, the calculated RDF rises up to 41000 in long
Hello,
My simulation crashed in the middle and I used the "-cpi checkpoint.cpt
-append" option to continue. However, GROMACS cannot continue and complains
about not being able to open the corresponding .trr file. I checked my
folder, the trr file is there and the name is the same as the *.tpr and
Hello,
I have two questions about using g_rdf:
1. Is it meaningful to calculate the radial distribution of water
molecules around a single atom of a surface residue, e.g. dangling OG1
oxygen of Threonine? (Does g_rdf takes care of the protein presence and the
excluded volume?)
2.
Hello,
I am trying to calculate the viscosity of my pure water system at 275K. The
system has run for 40ns. I issued the following command:
g_energy_d_mpi -f 275K_50_50_50_2.edr -s 275K_50_50_50_2.tpr -nmol 4202 -vis
sixsitewater_275K -b 0 -e 4
The numbers I get in the output file are
OMACS users
Subject: Re: [gmx-users] editconf
On 19/10/2010 12:22 PM, Payman Pirzadeh wrote:
> After rotation, wouldn't a minimization with very very small steps solve
the
> problem?
Only if the solute surface was very close to being symmetric about the
rotation axis. Since th
After rotation, wouldn't a minimization with very very small steps solve the
problem?
Paymon
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: October 18, 2010 7:14 PM
To: Discussion list for GROMACS users
Subject
Hello,
When we calculate the principal axes of protein, for each axis file, there
are 4 columns. The first one is the time (ps), but there are no descriptions
in the files about the rest. A little explanation will be very helpful.
Regards,
Payman
--
gmx-users mailing listgmx-users@gr
It does not explain for all files or all columns. For example, in the
evisco.xvg, the following lines are written, but there are 5 columns (one of
which is time). What are the rest? And the unit of the column (written
below) is not clear to me.
@title "Shear viscosity using Einstein relation"
: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: September 29, 2010 2:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation_2
On 2010-09-29 22.00, Payman Pirzadeh wrote:
> Adding to my previous comme
Spoel
Sent: September 29, 2010 1:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation
On 2010-09-29 20.52, Payman Pirzadeh wrote:
> Well, two questions:
>
> 1. My bulk values are fluctuating around 60 (I assume cP). But it looks
like
> very weird
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: September 29, 2010 1:03 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation
On 2010-09-29 20.52, Payman Pirzadeh wrote:
> Well, two questions:
>
> 1. My bulk values are fluctuati
list for GROMACS users
Subject: Re: [gmx-users] viscosity calculation
Payman Pirzadeh wrote:
> Hello,
>
> I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity
> of my system which is water. Two files are generate: *.xvg and the
> enecorr.xvg. Now, what
Hello,
I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity of
my system which is water. Two files are generate: *.xvg and the enecorr.xvg.
Now, what should I do to calculate the viscosity of my system with these two
files? Sorry for such naïve question.
Regards,
Payman
Hello,
This is the third time I am sending this e-mail, and I am not sure why it
does not show up on the list
I have a simulation from which I have the .edr, .xtc and .trr files. I want
to color my particles based on rmsd, potential energy, Sg (tetrahedral
parameter) or any other parameters
Your second guess is correct! I used grompp to restart (I had thought it
might provide me with the chance to change things if needed). I was
surprised initially when "cat" command did not work! The number of frames
were most of the time less than what it should be.
I also checked the 'trjcat -h'. I
Hi,
I read the wiki and manual on constraint and restraints, and I am still a
bit confused. But, my question is, should I remove the restraints after
equilibration in production phase?
What about constraints? How should I know my system really needs either of
them (is there a general rule or pr
>
> On Fri, 2009-08-28 at 16:41 -0400, Justin A. Lemkul wrote:
>> Payman Pirzadeh wrote:
>>> There is sth strange about this problem which I suspect it might be due
to
>>> the mdp file and input. I can run the energy minimization without any
>>> problems (I submi
There is sth strange about this problem which I suspect it might be due to
the mdp file and input. I can run the energy minimization without any
problems (I submit the job and it apparently works using the same submission
script)! But as soon as I prepare the tpr file for MD run, then I run into
th
: July 22, 2009 6:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
> Hello,
> I minimized the initial output (from another simulation) first; then I
> replicated it. This time, the minimization of the bigger box was done more
> easily!
cs.org]
On Behalf Of Payman Pirzadeh
Sent: July 22, 2009 9:22 AM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] genconf
Thanks a lot Mark! I will run the system for equilibration and then try to
replicate it. I will keep you guys posted.
Payman
-Original Message-
list for GROMACS users
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
> Yes and no!
> Sometimes there is an overlap, but sometimes I could find nothing! In the
> simplest case, how can we avoid overlaps in a way that the crystal
structure
> is maintained under pbc?
> Can th
romacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
> I am so sorry! I had sth in mind and I wrote sth else!!!
> My original box has zero charges and GROM
-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:25 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
> In my previous e-mail, I posted the amount of charge given by GROMACS:
>
>
gmx-users] genconf
Payman Pirzadeh wrote:
> OK! Thanks for the tips on thermostat.
>
> I multiplied my .gro file by using the command "genconf". My original
> box has non-zero charge, but the generated bigger box has some charges:
>
>
Define "non-zero." Is
OK! Thanks for the tips on thermostat.
I multiplied my .gro file by using the command "genconf". My original box
has non-zero charge, but the generated bigger box has some charges:
NOTE 2 [file sixsitemodel.top, line 8]:
System has non-zero total charge: -1.220703e-04
Then, during minim
...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 12:38 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> You were right! The dimensions of the box are zero in the .gro file.
Should
> I
romacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: Thursday, July 16, 2009 8:40 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] minimzation problem with a heterogeneous system
Payman Pirzadeh wrote:
> Hello,
> I have a configuration in which half of t
acs.org]
On Behalf Of Mark Abraham
Sent: July 16, 2009 12:39 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> You were right! The dimensions of the box are zero in the .gro file.
Should
> I change them to the values I have?
Set th
Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> But, I am using a .pdb file as the input of the gromacs. Does the
> preparation of pdb file differ from software to software?
>
It shouldn't, and I'm not 100% sure on how Gromacs handles
: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Hello,
> Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the
> rvdw cutoff to 10A, but problem was still there.
> Now I made my box bigger by using a visualization
el
> Sent: July 15, 2009 12:23 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] making a box of water
>
> Payman Pirzadeh wrote:
>> Thanks Justin.
>> Unfortunately, I realized that after I sent the e-mail. Anyways, I
started
>> running to models
I forgot to mention, the dimensions of current simulation box are: 27.154A*
31.354A* 103.386A
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 7:24 PM
To: 'Discussion list for GR
-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 12:23 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Thanks Justin.
> Unfortunately, I realized that after I sent the e-mail. Anyways, I started
> r
PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of David van der Spoel
> Sent: July 15, 20
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 2:38 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
> -Origi
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 2:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy of a box of water
Payman Pirzadeh wrote:
> Hi,
> I tested
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Thanks Justin.
> Unfortunately, I realized that after I sent the e-mail. Anyways, I started
> running to models: SPCE and TIP4P to check the energies of these systems
to
> figu
15, 2009 11:38 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Hi again,
> I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes
in
> the [atoms ]are specifies as opls_???, doesn't grompp check the
ayman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 10:14 AM
To: jalem...@vt.edu; 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] making a box of water
OK!
I changed my .top fil
o: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Will #include "ffgmx.itp" solve my problem? Would it be a general solution
> or in each case I should specify (if I add other solutes such as
proteins)?
>
Well, ffgmx is dep
emkul
Sent: July 14, 2009 7:07 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
You need to #include an appropriate force field that contains the
[defaults],
[atomtypes], etc. before you can define a [moleculetype].
-Justin
Payman Pirzadeh wrote:
> Here is my .to
users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 6:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Hello,
>
> I am trying to make a box of water from three different water models. I
> ca
Hello,
I am trying to make a box of water from three different water models. I can
make one from my own water model, but when I want to test TIP4P and SPCE, as
soon as it comes to energy minimization step and using grompp, I get the
following error message:
Program grompp, VERSION 4.0.4
Sourc
emkul
Sent: June 8, 2009 1:53 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote:
> Dear Justin,
> Here is the mpich version:
> MPICH Version: 1.2.7p1
> MPICH Release date: $Date: 2005/11/04 11:54:51$
> MPICH Patches ap
ginal Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:58 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> Well, when I set the box, I used &#
:56 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote:
> Hi Justin,
> Since the manual itself was not sufficient, I asked some other people who
> are running GROMACS in our group (but they run only on 2 CPUs). Here are
the
> steps I to
or GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> Here is the content of .itp file which I developed:
>
> ; This is an itp file to describe water's six-site model by H. Nada and
J.P.
> J. M. Van der Eerden, J. Chem. Phys. Vol.118, no.16, pp7401
an
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: June 8, 2009 11:12 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs on glacier
Payman Pirzadeh wrote:
> Hi,
>
> I had the c
romacs.org]
On Behalf Of David van der Spoel
Sent: June 8, 2009 11:13 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energies in simulation
Payman Pirzadeh wrote:
> To the best of my knowledge no, but how can I check that?
>
A. read the original paper: is your topology correct
simulation
Payman Pirzadeh wrote:
> Hi,
>
> I am using my own water model which I developed its .itp file. When
> simulation is done after 1ns and energy is kinetic and potential
> energies are analyzed, the kinetic value is almost OK, but the potential
> energy is almost
Hi,
I am using my own water model which I developed its .itp file. When
simulation is done after 1ns and energy is kinetic and potential energies
are analyzed, the kinetic value is almost OK, but the potential energy is
almost half of the value reported in literature and another MD code that I
am
Hi,
I had the chance to run the GROMACS 4.0.4 on another cluster. Same problem
still persists. But what I found is that it can be run on a node with 2
CPUs, but as soon as the number of nodes are increased to 2, 3, . it will
crash. Following are the last lines reported in different files:
"In the
aries. You also have make sure that you source the appropriate path to
mdrun in your script and that your GMXLIB path is correctly set.
Hope that helps,
Nicolas
Payman Pirzadeh a écrit :
> Hi Justin,
> Following is the script I use. But remember several points:
> 1. I compiled the g
g run at: `date`"
${MPIRUN} -np $NUM_PROCS -machinefile $PBS_NODEFILE -path
./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d -deffnm npttest
echo "Job finished at: `date`"
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@grom
s,
Tsjerk
On Tue, May 19, 2009 at 6:19 PM, Payman Pirzadeh
wrote:
> Hi All,
>
> Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
> yes, I will be appreciated if he/she can tell me how to run gmx on this
> facility. I either get error messages which says
Hi All,
Is there anyone who is running gromacs on glacier.westgrid.ca machine? If
yes, I will be appreciated if he/she can tell me how to run gmx on this
facility. I either get error messages which says either the executable or
the topology file can not be found.
Regards,
Payman
_
Hello,
When we use 'mdrun' or 'grompp' with the switch '-np' we specify the number
of nodes according to the manual. Does it mean if the nodes have 2
processors, then the simulation will be run on 4 CPUs or in -np we should
specify 4 instead of 2?
Payman
_
-users] make install-mdrun
Payman Pirzadeh wrote:
> Thanks Diego,
>
> But, the latest I found on downloads of gromcs webpage was 4.0.3! Is
> 4.0.4 somewhere else?
The homepage and wiki both have the links to 4.0.4, or you can simply change
the
ftp link to point to gromacs-4.0.4 inst
permissions in /usr/local/.
So, configure gmx to be installed in your local dir.
./configure --prefix=/global/home/pirzadeh/gmx404
On May 8, 2009, at 10:10 AM, Payman Pirzadeh wrote:
Hi All,
I realized that I am missing (Lib and bin folders) analysis tools and mdrun
MPI. I re-instal
Hi All,
I realized that I am missing (Lib and bin folders) analysis tools and mdrun
MPI. I re-installed the GROMACS 4.0.3, and I found that when I get to 'make
install-mdrun' the following messages show up ( I am just copying last
lines):
make[2]: *** [install-libLTLIBRARIES] Error 1
make[2]:
Hi Yanmei,
I had this problem with water molecules, and I found that any time I changed
the constrains without changing the boxes I generated through 'editconf'.
So, after changing the constrains, I had to redo all my box generation
process, then it was fine. But I ran into another problem and tha
Thank you very much.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: May 6, 2009 8:25 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] itp and gro files
Payman Pirzadeh wrote:
>
I was wondering if the order of sites in .gro file should be the same as in
.itp file.
Payman
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