yes. you need to and can still put System for the removal group.
>
> On Feb 21, 2012 5:51 PM, "xiaojing gong" wrote:
>>
>> Dear all,
>> I used the GMX 4.5.5 to run a simulation with a fixed plane and
water.
>> I wonder to know if I fix the plane, shall I use the command of
>> the remov
Hi,
The unit in output is in assumed to be for the standard unit input while the
value is in reduced unit.
So you need to do your own calculation to figure out what's the reduced unit
is.
Regards,
Yang Ye
On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang wrote:
> Dear all:
> I s
Please use "find" to locate FF.dat in your particular installation.
Regards,
Yang Ye
On Wed, Dec 1, 2010 at 12:17 PM, Jia Haitao wrote:
> Dear all,
> I have constructed a new CG force field named "polycg", and added them
> to direction ..$GMXLIB/polycg.ff. C
chive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Regards,
Yang Ye
--
gm
No way from MS. Check x2top.
Yang YE
On Mon, Mar 22, 2010 at 10:42 PM, 程迪 wrote:
> Hi,everyone
>
> I have build a SiO2 structure in Material Studio, And I've set the xyz
> coordinates and force field parameters of the structure. Is there some tool
> or method to produce a
ubscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Regards,
Yang Ye
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx
Just a work-around, force mpicc to point to cc.
alias mpicc=cc
Yang Ye
On Wed, Sep 16, 2009 at 5:35 PM, Mu Yuguang (Dr) wrote:
> No, even I do not use mpi , the error is still there.
>
>
>
> Regards
>
> Yuguang
>
>
> --
>
> *
Is LAM-MPI's binary in PATH? if you run mpicc from console, will it also
show "No such file or directory"? Check LAM-MPI installation.
Regards,
Yang Ye
On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) wrote:
> Hi,
> I use
> git clone git://git.gromacs.org/gromacs.gi
Get it through MacPorts? There is a free GUI frontend, porticus.
Yang Ye
On Tue, Dec 23, 2008 at 5:41 PM, Hadas Leonov wrote:
> Hi guys,
>
> Is there any intension to release binaries for Gromacs 4, for Mac OS X
> Leopard?
>
> Thanks,
> Hadas.
>
> =
3 1 1.00e-01 0.1
c0 is the distance in nm. for c1, put a relative large value to make it
stiff.
Yang Ye
On Tue, Dec 9, 2008 at 8:56 AM, Xin Liu <[EMAIL PROTECTED]> wrote:
> Yang Ye
>
> I can understand I need to put (3n-6) constraints to the system, but I
> do
www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/u
omacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't pos
; http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't p
grompp -np 16
On 11/21/08 7:06 PM, [EMAIL PROTECTED] wrote:
Hi All,
I'd need an help to run GROMACS 3.3.3 in parallel. I'm running mdrun in
parallel using the command:
mpirun -machinefile /storage1/home/rgr/machines_16 -np 16
/storage2/rgr/software/gromacs/bin/mdrun_d -s min0.tpr -g min0.log -
Can anyone of you tell me what is the reason for that?
>
> Thank you in advance.
>
> Yang
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the arch
Writing on local or remote certainly makes a difference. How about the speed
with no output at all?
Regards,
Yang Ye
From: xianghong qi <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Sunday, November 9, 2008 12:36:40 AM
Subject: Re
More details please.
Local hard disk?
How much the time difference?
YY
On 11/8/08 12:41 PM, xianghong qi wrote:
Hello, all:
I compare the two simulations with different output frequency for .xtc
file in same machine. One with low frequency runs much faster than
the one with high frequency.
version for all analysis
programs.
Regards,
Yang Ye
On 10/30/08 11:40 AM, Chih-Ying Lin wrote:
Hi
Here is my pdb file.
#!/bin/bash
#PBS -l nodes=2
cat $PBS_NODEFILE
echo Working directory is $PBS_O_WORKDIR
cd $PBS_O_WORKDIR
mpirun -np 2 g_energy_mpi -f minim_ener.edr -o minim_ener.xvg
miss anything in the tutorial/example? Read the manual more
carefully to understand how grompp works. This list just tries to help
any user but not spoon-feed.
Regards,
Yang Ye
On 10/24/08 3:19 PM, wang wrote:
Dear
Sir ,
I used your CG parameters and gromacs V3.3 to simulate protein
aggregation
this secondary trajectory.
Regards,
Yang Ye
- Original Message
From: #NGUYEN CONG TRI# <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Monday, October 13, 2008 3:47:32 PM
Subject: [gmx-users] Selecting part of the trajectory
Hi all,
I want get the snapshots eve
This is normal. You shall get statistical identical properties between runs.
Besides obvious reasons (gen_vel=yes and gen_seed=-1, or
optimize_fft=yes), there might be other factors.
Regards,
Yang Ye
On 9/22/08 8:26 AM, xuji wrote:
> Hi all:
> I run mdrun of gromacs-3.3.3 6 times of a
there is dpdmacs available..
Regards,
Yang Ye
- Original Message
From: Suman Chakrabarty <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users
Sent: Monday, September 1, 2008 5:50:15 PM
Subject: [gmx-users] Dissipative Particle Dynamics (DPD)
Dear all,
since one of my
A more complete answer is that to define energy groups for this reside and rest
residues respectively, generate the tpr with grompp and then use mdrun -rerun
to run through the existing trajectory to obtain what you wanted.
Regards,
Yang Ye
- Original Message
From: Justin A. Lemkul
successfully
Only 0 energies in the log file
Can I ignore above error messages?
Most likely. I checked those errors before and they are indeed not
errors. gmxtest suite is not just not very up-to-date with gromacs.
Thank you in advance.
Regards,
Teru
2008/8/7 Yang Ye <[EMAIL PROTEC
experience with
OpenMPI.
Regards,
Yang Ye
ikedaike wrote:
Hi
I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS
4.5(Intel Core2 Duo).
I tested with gmxtest-3.3.3 and all tests passed in non-parallel.
However, when I tested in parallel, I encountered the following messages.
[Use 2 Cores
ating density) or the template.
To understand some development work for Gromacs (not only analysis
tools), I recommend Erik's talk in CSC2007.
http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007
"Thursday 1.3. Workshop day 3" *Gromacs development.*
Regards,
Yang Ye
David van der Spoel wrote:
Mu Yuguang (Dr) wrote:
Dear All,
When I try to simulate TIP4Pew water box at 298K, and found the density
got from gromacs is relative low (983 g/cm3) than the amber (sander)
version 994 g/cm3. I cannot find the reason. The parameters for the
tip4pew model are identical
[EMAIL PROTECTED] wrote:
Dear colleagues,
I successfully finished a 3 ns gromacs run using 40
nodes. When, I tried to convert .trr file to .xtc using trjconv, the
run stops at 560 frame giving error "cannot determimine precision of
trn file". I tried various options like -s
It could be system-specific. Could you try out dppc in tutor/gmxbench or
download gmxbench from gromacs' website (section Benchmark)?
Regards,
Yang Ye
Dr. Bernd Rupp wrote:
same problem as mpich2.
regards,
Bernd
Am Mittwoch, 25. Juni 2008 schrieb Yang Ye:
I don't think Pytho
I don't think Python is to be blamed.
How about lam-mpi?
Regards,
Yang Ye
Dr. Bernd Rupp wrote:
Dear all,
CPU: Intel(R) Core(TM)2 Extreme CPU Q6850 @ 3.00GHz
System: fedora 8
Kernel: 2.6.25.6-27.fc8 #1 SMP
gromacs 3.3.3 correct compiled
MPI : mpich or mpich2
We had the same problem
For latest stable 3.3.3, there is no multi-thread implementation.
For CVS version for coming 4.0, might be, I am not sure, but that's only
for testing.
Your question tricky without indicating the version.
Regards,
Yang Ye
Lee Soin wrote:
But I see that in mdrun there's an option
this topic. So I think it's maybe better we
discuss this problem in private email.
I think Yang Ye simply meant that you should choose a meaningful subject -
not "Re: [gmx-developers]". I also forward this to the users mailing list,
which is the best place for this discus
there's no other
>> people that is interest in this topic. So I think it's maybe better we
>> discuss this problem in private email.
>>
> I think Yang Ye simply meant that you should choose a meaningful subject -
> not "Re: [gmx-developers]". I als
p and then center that group.
Regards,
Yang Ye
Anamika Awasthi wrote:
Dear All,
Please tell, what should I predict from this graph?
I can understand this is normal type of graph.
Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, becaus
Hi, beibei
The first point made by Mark is to check whether volume stabilizes when
the system is subjected to NPT simulation.
Regards,
Yang Ye
Mark Abraham wrote:
> Please leave GROMACS-related correspondence on the GROMACS mailing list.
> That way others can follow and contribute
What are the atoms involved in the Long Bond waring?
For cyclic peptide, you also need to hand edit the topology file after
pdb2gmx to connect the last residue to the first residue.
Regards,
Yang Ye
David van der Spoel wrote:
N-J.M. Macaluso wrote:
Hello,
I am using the Amber ports for
://www.wwpdb.org/documentation/format23/sect9.html
The same applies to GRO file, which is described in GROMACS manual.
Regards,
Yang Ye
andrea spitaleri wrote:
Hi,
have look to this:
http://stein.bioch.dundee.ac.uk/~charlie/software/pdb-mode/pdb-mode.html
I found it very useful
regards
andrea
tware installation (Linux) and configuration on network and
LAM-MPI libraries.
Regards,
Yang Ye
之光 贾 wrote:
> ASUS DSBV-DX/C or Intel S5000VSA
> E5410 2.33 * 2
> FB-DIMM 1G * 8...
>
> I could only find some body test their E5410 on Gromacs in google, but
> I am not sure this
with pcoupl=none
Arnab Senapati wrote:
-
Hi,
can anyone tell me how to run a NVT simulation in gromacs.
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http:
one node, more
cores are better. This happens to be my case.
If 32-core or more parallel running is planned, 2.8GHz helps.
Regards,
Yang Ye
andrea spitaleri wrote:
Hi all,
we are going to buy a new cluster and we are in doubt about the frequency to
consider.
Basically, we have the possibility
gards,
Yang Ye
Low Soo Mei wrote:
Hi gmx-users,
If I use different position restraints during each stage of
minimization, should I separately write all my restraints in the same
.top file in this manner,
#ifdef LIPID_ALL_POSRE
#include "lipid_all_posre.itp"
#ifdef WATER
Mark Abraham wrote:
Collins Nganou wrote:
Dear all.
greetings. I need to know what force fields can I Choose to run:
1- ethanol vibrational mode.
2- B-DNA with 15 base pairs
Start with a literature search. You'll need to do one later in order
to defend your choice. "Some person on a mailing
You can opt for 3).
If your system only compose of nanotube and water, why freeze it?
Regards,
Yang Ye
tuyusong wrote:
Hi, all,
I have a system with one carbon Nanotube and lots of water,
in which Nanotube is frozen. How do I remove the center-of-mass:
1) only
different mdp files with different ref_t.
Regards,
Yang Ye
- Original Message
From: s lal badshah <[EMAIL PROTECTED]>
To: gromacs
Sent: Monday, March 31, 2008 12:48:47 PM
Subject: [gmx-users] Simulation at different temperature
Dear Experts,
Hi ! I want to simulate a protein a
if
;include"disres.itp"
Putting semicolon in front of the line effectively turns off that line.
Regards,
Yang Ye
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive a
Please supply us the output of trjconv.
Alternatively, use trjconv -o foo.pdb -sep.
Regards,
Yang Ye
齐文鹏 wrote:
>
> I use the trjconv -split 1.0 to split my long xtc file to seperate pdb
> files to analysis with the Curves .
>
> But I cannot split files more than 1020. why? The
ave a solution for almost all molecules.
Regards,
Yang Ye
Xiangyu Fan wrote:
Hi all,
I am using GAFF force field for Gromacs package to simulate MD of
surfactant molecule. I know we can generate .top file using some
simple command like pdb2gmx if we use gromos force field. I am just
wondering wh
trjconv -dump time
Huey Ling Tan wrote:
Hi All,
I wonder if anyone knows what is the command to use in order to
generate .gro files for a certain time-step interval in a simulation?
For example, if I have a completed simulation of 10 ns long and I want
to output (somehow) 10 .gro files each
Ricardo Soares wrote:
Hi everybody,
I think this may sound rather trivial for most users, but I intend to
install gromacs 3.3.1 on a dual core machine and I want to be sure
what to do. Could anyone indicate me some online tutorial to do so (as
well some simulation examples)? Is this conside
i reckon that you have not built in mpi support to mdrun in GROMACS so
each instance of mdrun produces one trajectory rather than running in
parallel and produce only one trajectory.
Mark Abraham wrote:
Yunierkis Perez Castillo wrote:
Hi all, I'm new to gromacs. I have setup a protein MD simul
posting for my friend as her network has some problem.
Dear gmx-users, I want to simulate lipid bilayers at temperature as low as
230K, will the water near the head group of lipid freeze? If I want to get a
knowledge of the phase of lipid at temperature much lower than zero, what
should I
you shall check what this warning message claims first.
Mao-Cai Yan wrote:
> Dear colleague,
> I want to calculate the Coul-SR energy and LJ energy between the
> receptor and PART of my ligand, using a given XTC file with "mdrun
> -rerun". I modified "energygrps" in the MDP file, and then type
> g
shall you find them yourself first?
/src/mdlib/*fft*
Actual FFT is done by FFTW.
Regards,
Yang Ye
xuji wrote
Protein are defined by the residue names inside aminoacids.dat. So, it
is possible for nucleic acid to be "Protein".
Steven Kirk wrote:
Mark Abraham <[EMAIL PROTECTED]> wrote
Subject: Re: [gmx-users] Re: Targeted MD
To: Discussion list for GROMACS users
Message-ID: <[EMAIL PROTECTED]>
Conten
wei-xin xu wrote:
2008/1/10, Mark Abraham <[EMAIL PROTECTED]>:
Some hints on
practices that generally not a good idea to use:
Do not use
separate thermostats for different components of your system. Some
molecular dynamics thermostats only work well in the thermodynamic
limit. If y
gromacs manual has the answer (FF terms) for you.
Subhashis Biswas wrote:
Hi,
I know this issue has been discussed in some form before, but hough
may be I resurface it again. Is it possible to transfer a UFF
forcefield to a GROMACS forcefield with help of a script? UFF
force-field cannot be
Use mdrun -rerun (will not be a complete recovery).
pragya chohan wrote:
Dear users
I by mistake deleted the edr file generated from production run. Is
there any way to recover or generate the edr file again?
It's abou
1. how long is the simulation?
2. did you start from equilibration (with gen_vel=yes) or production md?
3. ...
On 12/5/2007 8:28 PM, Dechang Li wrote:
> Dear all,
>
> I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p).
> I run two similar simulations, one for 2 cpu
you shall use AMBER's
new2oldparm < new > old
to get the old format file.
I remember that David Mobley has another ambconv script on his website
(http://www.alchemistry.org/) but it is not accessible right now.
Regards,
Yang Ye
On 12/6/2007 3:52 AM, Shozeb Haider wrote:
Hi,
I a
Hi,Zhou Bo
Please take some time to get to know what's 1-4 interaction, and what is
torsion.
In simple words, they are of two types: 1-4 belonging to non-bonded
interaction; torsion is bonded interaction. So in nature, they are not
conflicting each other; The reason why we isolate the definition
On 11/21/2007 7:33 PM, Vasilii Artyukhov wrote:
Hi everybody,
Sorry for a somewhat technical question, but I'd like to know which is
the best way to run GROMACS on a SMP machine (in particular, a
multicore PC). The (known) points of interest are:
- Does GROMACS support multithreaded executi
o, you can use this mechanism to do position restraint
MD with different parts of the system, or gradually give freedom to the
system.
Regards,
Yang Ye
On 11/20/2007 4:18 PM, Maik Goette wrote:
Hi
Use the following term in your mdp:
define = -DPOSRES
Now, everythi
step 4) shall be add water, minimize energy.
step 5) it's a bad idea to couple ion alone, see wiki pls.
step 6,7) you shall at least have two stages, em, eq before production md.
On 11/19/2007 5:23 AM, Peggy Yao wrote:
Hi all,
I would like to simulate a protein with calcium ions at the calcium
submitting a bugzilla entry could be helpful in examining this case.
On 11/17/2007 4:45 AM, Amadeu wrote:
My student and I have been trying the latest Gromacs version (3.3.2)
for the simulation of a CNT. We noticed that the bonded energies
calculated with 3.3.2 are quite different compared to
Find out the c preprocessor of the Compaq C compiler and try to obtain
its output of parsed C source file.
On 11/15/2007 10:12 AM, [EMAIL PROTECTED] wrote:
I have had some success reproducing the event with a simple c program
and the issue appears to be with the in-house mpicc wrapper script.
ine, so you may go into the files to hard code the string values
(e.g. GMXLIBDIR are present in tools/futil.c and kernel/topio.c)
Regards,
Yang Ye
On 11/15/2007 6:59 AM, Chris Neale wrote:
I am having difficulty installing the mpi version of gromacs 3.3.2 on
a new computer. I have the same pro
You can send me the file off the list. To solve this kind of problem,
start from simple case: two or a handful of atoms.
Regards,
Yang Ye
On 11/13/2007 5:36 AM, Dongsheng Zhang wrote:
Dear Yang Ye,
Thank you very much for your reply. You are very helpful in my
experience. I turned off the
how do you turn off the interactions? e.g. setting rvdw=0 doesn't mean
turning of vdw interactions.
Regards,
Yang Ye
On 11/13/2007 12:55 AM, dongsheng zhang wrote:
Dear Mark,
The installation works for other systems. The error happens in either EM or
MD. When I turn off all intera
ribe from the group
*/Yang Ye <[EMAIL PROTECTED]>/* wrote:
it could not be possible since amber force field doesn't
parameterized
NLYN. alternative, use ACE/NME to cap the peptide.
On 11/9/2007 7:36 PM, Hu Zhongqiao wrote:
>
> Hi,
>
>
>
this is a too general question. please read the wiki first.
On 11/9/2007 9:58 PM, Kitty Ji wrote:
> Dear users:
> After we get some data from GMX simulation, how can we validate them?
> I met many difficulties in parameters setting.
> ___
> Kitty JI
> Groupe
On 11/9/2007 9:21 PM, David van der Spoel wrote:
Yang Ye wrote:
On 11/9/2007 9:09 PM, David van der Spoel wrote:
Yang Ye wrote:
On 11/9/2007 6:47 PM, Bruce Milne wrote:
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds
ACE for the N-termail and NME for the C-terminal. They are neutral. You
can do so with aids from PyMol...
Regards,
Yang Ye
On 11/9/2007 9:50 PM, Hu Zhongqiao wrote:
Thanks, Yang Ye.
You mean that I put an additional ACE or NME on the N-terminal lysine
residue?
zhongqiao
Message: 3
On 11/9/2007 9:09 PM, David van der Spoel wrote:
Yang Ye wrote:
On 11/9/2007 6:47 PM, Bruce Milne wrote:
Dear Li Qiang,
it seems another guy get the same error(cannot pass gmxtest with
rb1/acetonitrilRF) as me. and it sounds like the compatible problem
between GROMACS 3.3.2 and and UBUNTU
about their failure pattern when reporting.
The fix of acetonitrilRF is available in the CVS. Even you don't apply,
it won't affect if you are using parallel and you are not using RF.
Regards,
Yang Ye
On 11/9/2007 7:49 PM, Li Qiang wrote:
I see. thanks for the information.
but
found that it was due to one line in mshift.c
"srenew(g->edge[0],n); "
mdrun output:
realloc for g->edge[0] (24 bytes, file mshift.c, line 251,
g->edge[0]=0x0x 1)
Regards,
Yang Ye
Cheers,
Bruce
___
gmx-users m
it could not be possible since amber force field doesn't parameterized
NLYN. alternative, use ACE/NME to cap the peptide.
On 11/9/2007 7:36 PM, Hu Zhongqiao wrote:
Hi,
I am using amber force field in Gromacs. The protein I simulated is
the lysozyme (PDBID: 1HEL). I want to set all lysine
Regarding the failed test for simple/rb1, I used dmalloc and the message is
realloc for g->edge[0] (24 bytes, file mshift.c, line 251,
g->edge[0]=0x0x 1)
the line in mshift.c is
srenew(g->edge[0],n);
Regards,.
Yang Ye
On 11/9/2007 1:35 AM, David van der Spoel wrote:
Yang
3.3.1
---
Program mdrun, VERSION 3.3.2
Source code file: network.c, line: 437
Routine should not have been called:
gmx_sumi
---
Perhaps gmx-developer is a better place for this thread.
Regards,
Yang Ye
file
GMXRC.bash in the locations which you can find in "make install".
Run it with
source /path/to/GMXRC.bash
Then you can make sure that you are using your own version.
Put that line "source ..." into ~/.bashrc shall make it default for
every login session.
Regards,
Hi,
You shall always try to build gromacs yourself. What's the error with
tutorial?
Regards,
Yang Ye
On 11/7/2007 10:14 AM, Li Qiang wrote:
hi all,
I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package
Manager(SPM). However, it can not pass the gamxtest with log as below
between ligand and protein,
how about other propery of covalent bond? Maybe I
missed something of your message.
Yours
Tanping
--- Yang Ye <[EMAIL PROTECTED]> wrote:
you might want to try distance constraint.
On 11/7/2007 5:11 AM, Tanping Li wrote:
Dear all,
I searched the maillin
you might want to try distance constraint.
On 11/7/2007 5:11 AM, Tanping Li wrote:
Dear all,
I searched the mailling list, and still can't find a
way to set up my system: a ligand covalently bond to
protein.
I don't know if there is a easier way to do this. What
I can think of is:
1) Add a b
Hi,
To use GROMACS' spc topology with ffamber, you may create a new spc
topology, e.g. spc-amber.itp. Following is its content. If you know C
preprocessor, you can merge it with original spc.itp.
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; nr type resnr residue atom cg
I doubt that no one could give you such script.
To plot free energy surface, you can utilize Rg/Q or Rg/ContactNumber or dPCA
(http://wiki.gromacs.org/index.php/Dihedral_PCA) analysis.
Regards,
Yang Ye
- Original Message
From: xi zhao <[EMAIL PROTECTED]>
To: gmx-users@groma
Doing position-restrained simulation is useful to equilibrate solvent and ions.
If you would like to study the dynamics of the peptide, PRMD doesn't help. PRMD
is usually performed before production run for a duration from several hundred
ps to 1ns.
Regards,
Yang Ye
- Original Me
submit a bug report at bugzilla.gromacs.org?
On 10/17/2007 2:40 AM, Justin A. Lemkul wrote:
Hello all,
I am having a strange error when using pdb2gmx. I am trying to generate the
topology for a simple protein, using Gromos96 43a1. I am able to create the
topology with version 3.3 without issu
On 10/16/2007 2:31 AM, tangxuan wrote:
Dear all,
If pbc is full or xyz in mdp file, do i need to use the "trjconv -pbc
nojump" to remove the jump when the protein is separate in the box after
simulation and I want to calculate the rmsd of the protein?
IT is not necessary to use trjconv -pbc be
with explicit solvent.
Regards,
Yang Ye
On 10/15/2007 12:24 AM, OZGE ENGIN wrote:
Sorry, but I have to ask some more questions. I have just started to perform
simulations in vacuum. I can understand not using of PME in vacuum simulations;
however, I can not understand the sentence you
Program like VMD can draw extra bond. You need to get its manual and
code a line or two in TCL.
Regards,
Yang Ye
On 10/14/2007 11:38 PM, van Bemmelen wrote:
Hi Ozge,
I'm not sure what you mean by "visualization". But what about using VMD
for trajectory visualization
y done without PBC, Rotation is recommended.
>> COM velocity removal's effect is directly visible, so if "Linear" works for
>> you, you may use it.
Thanks in advance
Ozge
-Original Message-
From: Yang Ye <[EMAIL PROTECTED]>
To: Discussion list for GROMAC
in the beginning of your simulation for a few ns.
Regards,
Yang Ye
- Original Message
From: Dechang Li <[EMAIL PROTECTED]>
To: gmx-users
Sent: Sunday, October 14, 2007 5:34:35 PM
Subject: [gmx-users] the comm_mode
Dear all,
There are three options of comm_mode:
On 10/4/2007 11:50 PM, maria goranovic wrote:
Dear All,
- So I "think" I succeeded in running gromacs on a 4-core node. How
does one confirm this without looking at the speed. i.e, where is it
mentioned in the log file what the number of processors is ? I do get
4 different log files for 4 pr
Hi,
For average distance, you can gather distance v. time by g_mindist, then
average them.
For "average energy", you are refering to interaction energy? What you can do
is to define two energy groups for two residues separatedly, make a new tpr and
use mdrun rerun to get it.
Reg
gy of small molecules in OPLS format but except this,
don't use for serious business.
Regards,
Yang Ye
On 10/2/2007 6:58 PM, [EMAIL PROTECTED] wrote:
Hi,
On the gromacs webpage in user contributions->topologies you have (at
least) 2 forcefields do download that allow you to simulate N
the amber port from eric j sorin.
On 10/2/2007 6:44 PM, Monika Sharma wrote:
Dear All,
I want to start nucleic acid simulations. I am using gromacs3.3.1. But
I could not find any mention of Nucleic Acids in any of the
force-field provided by gromacs distro. So does it mean that one _can
not_
to
GROMACS. The amb2gmx.pl from E.J. Sorin shall help
(http://chemistry.csulb.edu/ffamber/tools.html).
Regards,
Yang Ye
On 9/29/2007 10:22 PM, Dechang Li wrote:
> Dear gmx-users，
> I want to use ANTECHAMBER & GAFF to generate the topology of a small
> molecular(HIV-1 Protease inh
On 9/29/2007 9:13 PM, Lorenzo Isella wrote:
Dear All,
I am 100% new on this list and to Molecular Dynamics in general.
This is what I am interested into (and would like to know if Gromacs is
then the right tool).
I am not really into biology or chemistry, but rather in aerosol science.
I am inter
make shall automatically recognize the newly modified file and you just
need to type make.
If it says nothing to do, you just need to delete the file.o of your
modified source file and then type make.
Anyway, make clean && make will do so.
Also, if you are changing tool part, then you just need
Perhaps you shall look Espresso (http://www.espresso.mpg.de/) for
coarse-grain simulation. Espresso saved my PhD thesis after spending
more than one year's time in engaging GROMACS to do what I desired.
Because of the size of the colloid simulation system, the expensive PME
calculation will dr
shall you try -fit progress?
On 9/25/2007 11:03 PM, [EMAIL PROTECTED] wrote:
Hello gmx-users!
I am trying to make a simulation video in which a water droplet is
rolling or sliding on a surface. Due to a periodic boundary conditions
a droplet is not whole all the time but it disappears from the
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