Re: [gmx-users] installation problem of gromacs binary
- Original Message - From: priyabrata panigrahi priyabra...@gmail.com Date: Friday, August 20, 2010 16:56 Subject: [gmx-users] installation problem of gromacs binary To: gmx-users@gromacs.org I was trying to install gromacs-3.3.3-1.x86_64.rpm. I got the following error error: Failed dependencies: fftw3 = 3.0.1 is needed by gromacs-3.3.3-1.x86_64 libfftw3f.so.3()(64bit) is needed by gromacs-3.3.3-1.x86_64 I installed fftw-3.2.2.tar.gz. Mixing RPM and source distributions doesn't really work, because the RPM database is unaware of anything you've done outside RPM. Either install a *single-precision* FFTW3 RPM, or GROMACS also from source. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] installation problem of gromacs binary
On 2010-08-20 09.14, Mark Abraham wrote: - Original Message - From: priyabrata panigrahi priyabra...@gmail.com Date: Friday, August 20, 2010 16:56 Subject: [gmx-users] installation problem of gromacs binary To: gmx-users@gromacs.org I was trying to install gromacs-3.3.3-1.x86_64.rpm. I got the following error error: Failed dependencies: fftw3 = 3.0.1 is needed by gromacs-3.3.3-1.x86_64 libfftw3f.so.3()(64bit) is needed by gromacs-3.3.3-1.x86_64 I installed fftw-3.2.2.tar.gz. Mixing RPM and source distributions doesn't really work, because the RPM database is unaware of anything you've done outside RPM. Either install a *single-precision* FFTW3 RPM, or GROMACS also from source. Mark And, obviously, you might want to consider a newer gromacs version. For quite a few distributions you can use yum or apt-get gromacs. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sorient
Dear all when i try to run g_sorient with g_sorient -f prod_full.xtc -s prod.tpr -o ANALYSIS/sorie nt/sori.xvg -no ANALYSIS/sorient/snor.xvg -ro ANALYSIS/sorient/sord.xvg I am getting a segmentation fault what would be the problem could anyone help in in this regard E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] sampled distances
Chris Again sorry for the delay. I posted a couple of times but the attachment was too big so I had to compress the file. Here is the histogram for the sampled distances. As you can see they are well behaved below 2nm, whereas above they are not. The histogram for the previous distance vs time plot is the brown coloured curve centred at 2.35 nm. Cheers Gavin histo.ps.bz2 Description: application/bzip -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Trajectory protonation and inter proton distance calculation
It seems that my messages still are not getting through. I'll try again to post this today, apologies if you're getting multiple... Johannes Beck wrote: Dear Justin, dear all, thank you for your reply. Running protonate without defining an index file via -n is indeed possible, but when the groups are to be chosen after calling protonate, only a group named Protein that contains 82 residues was offered, but no group containing 124 residues, as I wished to get for the protonated molecule: -- protonate -s 65300.gro -f md.xtc -o md_protonated.xtc That is exactly what you want - to protonate your protein, which currently has 82 atoms. I have no idea about what the help information is talking about (probably a more advanced application), but as for doing a simple protonation like this one, your command is correct. snip Is the trajectory I now received (md_protonated.xtc) properly protonated? How could I check this? For application of g_dist on this Use gmxcheck. It will report the number of atoms in the trajectory. protonated trajectory, a run input file (.tpr) that corresponds to the protonated state seems to be required. If the run input file from the unprotonated MD trajectory is given as input in g_dist, g_dist fails and suggests to use tpbconv in order to convert the original run input file into a run input file for the protonated state. I wonder how I could use tpbconv to do that? tpbconv is only useful for making a subset of the original .tpr file, not for adding atoms to it. You can protonate the configuration in the .tpr file using protonate, but the output can only be a coordinate file or trajectory, not a .tpr file. You will likely have to produce a new topology for your now-protonated system that corresponds to the trajectory. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
Hi there,
Now I have some results that I hope to clear this matter about dihe funct 4
and 9 (specially the latter).
Please see:
http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
From my understanding (and results), where dihe funct 4 or 9, replacing both
with 1 changes nothing in tot pot energy for amber force fields.
I don't know about charmm here, but I thought amber dihe parameters were
sort multiple terms and as far as I remember, the need to convert proper
dihe to RBs was necessary for early versions of gromacs 3.x, am I right?
Best,
Alan
On 18 August 2010 22:01, Alan alanwil...@gmail.com wrote:
Hi Berk and Mark,
Erik was too lazy to document this, I now added it to the manual.
Is this manual available even via git? When funct 4 and 9 appeared? in gmx
4.5?
Type 4 is identical to type 1, it is only there to distinguish improper
from proper dihedrals.
So for amber impr. dih. only, if I put 1 instead of 4 I for my GAFF
generated ligand it would do the same thing, right? I ask that for the grace
of compatibility with gmx 4.0.x.
Type 9 is identical to type 1, except that multiple entries in
dihedraltypes will lead to
multiple functions on one dihedral.
This one is more difficult to get. I know about multiple entries in CNS,
Charmm and Amber. I was even trying to convert amber99bsc0 new dih
parameters to gromacs and I was using funct 1. However I didn't have Amber
to validate, and now I have Amber11, I don't have time for the moment.
Sounds like funct 9 is to not only pave the way for Charmm, but may help to
address properly the bsc0 parameters, right?
But I need to understand this better. Converting amber's proper dih. param.
to gromacs 4.0.x was done by making these dih. to be RB. However
amb2gmx.pl converts everything to proper (using funct 1) -- acpype is
smarter here. So in gmx 4.0.x proper dih. funct 1 was never able to
interpret multiple entries on one dihedral?
Now on Mark:
Type 9 was added to facilitate CHARMM's multiple proper dihedrals, in git
commit a7c597c778351f by Erik, whose message was
Added support for dihedraltype 9, which allows multiple terms for
proper dihedrals.
By listing a dihedral with type 9, grompp will now scan the force field
to see if there are
multiple terms on _adjacent_ lines listed in the dihedraltypes section,
and in that case add them all.
A code snippet in src/kernel/toppush.c reads
if(ft == 9)
{
/* Previously, we have always overwritten parameters if
e.g. a torsion
with the same atomtypes occurs on multiple lines. However,
CHARMM and
some other force fields specify multiple dihedrals over
some bonds,
including cosines with multiplicity 6 and somethimes even
higher.
Thus, they cannot be represented with Ryckaert-Bellemans
terms.
To add support for these force fields, Dihedral type 9 is
identical to
normal proper dihedrals, but repeated entries are allowed.
*/
bAllowRepeat = TRUE;
ft = 1;
}
So amb2gmx.pl never worked properly here? For example, I have this for DNA
with amber99bsc0:
; treated as usual propers in GROMACS since Phase angle diff from 0 or 180
degrees
; i j k l func phase kd pn
2 3 6 23 1 190.98 4.92892 1 ;O5'- C5'- C4'- C3'
2 3 6 23 1 295.63 0.38535 2 ;O5'- C5'- C4'- C3'
2 3 6 23 1 348.10 4.02848 3 ;O5'- C5'- C4'- C3'
28 29 32 33 131.80 0.77480 1 ;O3'- P- O5'- C5'
28 29 32 33 1 351.96 5.25733 2 ;O3'- P- O5'- C5'
28 29 32 33 1 357.25 1.48473 3 ;O3'- P- O5'- C5'
So, this would only work if funct was 9 and not 1 as above? The way it is,
the last line of a sequence dih. is overwriting the 2 previous one, ignoring
them completely?
From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it
can be seen that dihedraltypes 4 and 1 call the same evaluation function.
Perhaps Erik can confirm this.
src/gmxlib/ifunc.c did suggest to me that something is not quite right...
def_bonded (PDIHS,Proper Dih., 4, 3, 3, eNR_PROPER, pdihs
),
def_bonded (RBDIHS, Ryckaert-Bell., 4, 6, 6, eNR_RB, rbdihs
),
def_bonded (FOURDIHS, Fourier Dih.,4, 4, 4, eNR_FOURDIH, rbdihs
),
def_bonded (IDIHS,Improper Dih., 4, 2, 2, eNR_IMPROPER,idihs
),
def_bonded (PIDIHS, Improper Dih., 4, 3, 3, eNR_PROPER, pdihs
),
If PIDIHS is an improper dihedral with the functional form of a proper
dihedral, should it not use eNR_IMPROPER?
I definitely need to run my validations myself, but any words here would be
helpful.
Many thanks you all.
Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry,
RE: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
Hi,
That depends.
If you have explicit parameters in the dihedral section then 1 and 9 are
equivalent.
If grompp has to look up parameters in the dihderaltypes section there will be
difference
when multiple parameter lines are present the same atom types for a dihedral
type 9.
Berk
From: alanwil...@gmail.com
Date: Fri, 20 Aug 2010 14:41:33 +0100
To: gmx-users@gromacs.org
CC: gporte...@mmb.pcb.ub.es
Subject: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
Hi there,
Now I have some results that I hope to clear this matter about dihe funct 4 and
9 (specially the latter).
Please see:
http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
From my understanding (and results), where dihe funct 4 or 9, replacing both
with 1 changes nothing in tot pot energy for amber force fields.
I don't know about charmm here, but I thought amber dihe parameters were sort
multiple terms and as far as I remember, the need to convert proper dihe to RBs
was necessary for early versions of gromacs 3.x, am I right?
Best,
Alan
On 18 August 2010 22:01, Alan alanwil...@gmail.com wrote:
Hi Berk and Mark,
Erik was too lazy to document this, I now added it to the manual.
Is this manual available even via git? When funct 4 and 9 appeared? in gmx 4.5?
Type 4 is identical to type 1, it is only there to distinguish improper from
proper dihedrals.
So for amber impr. dih. only, if I put 1 instead of 4 I for my GAFF generated
ligand it would do the same thing, right? I ask that for the grace of
compatibility with gmx 4.0.x.
Type 9 is identical to type 1, except that multiple entries in dihedraltypes
will lead to
multiple functions on one dihedral.
This one is more difficult to get. I know about multiple entries in CNS, Charmm
and Amber. I was even trying to convert amber99bsc0 new dih parameters to
gromacs and I was using funct 1. However I didn't have Amber to validate, and
now I have Amber11, I don't have time for the moment.
Sounds like funct 9 is to not only pave the way for Charmm, but may help to
address properly the bsc0 parameters, right?
But I need to understand this better. Converting amber's proper dih. param. to
gromacs 4.0.x was done by making these dih. to be RB. However amb2gmx.pl
converts everything to proper (using funct 1) -- acpype is smarter here. So in
gmx 4.0.x proper dih. funct 1 was never able to interpret multiple entries on
one dihedral?
Now on Mark: Type 9 was added to facilitate CHARMM's multiple proper
dihedrals, in git commit a7c597c778351f by Erik, whose message was
Added support for dihedraltype 9, which allows multiple terms for proper
dihedrals.
By listing a dihedral with type 9, grompp will now scan the force field to
see if there are
multiple terms on _adjacent_ lines listed in the dihedraltypes section, and
in that case add them all.
A code snippet in src/kernel/toppush.c reads
if(ft == 9)
{
/* Previously, we have always overwritten parameters if e.g. a
torsion
with the same atomtypes occurs on multiple lines. However,
CHARMM and
some other force fields specify multiple dihedrals over some
bonds,
including cosines with multiplicity 6 and somethimes even
higher.
Thus, they cannot be represented with Ryckaert-Bellemans terms.
To add support for these force fields, Dihedral type 9 is
identical to
normal proper dihedrals, but repeated entries are allowed.
*/
bAllowRepeat = TRUE;
ft = 1;
}
So amb2gmx.pl never worked properly here? For example, I have this for DNA with
amber99bsc0:
; treated as usual propers in GROMACS since Phase angle diff from 0 or 180
degrees; i j k l func phase kd pn 2 3 6 23 1 190.98
4.92892 1 ;O5'- C5'- C4'- C3'
2 3 6 23 1 295.63 0.38535 2 ;O5'- C5'- C4'- C3' 2 3
6 23 1 348.10 4.02848 3 ;O5'- C5'- C4'- C3' 28 29 32 33
131.80 0.77480 1 ;O3'- P- O5'- C5'
28 29 32 33 1 351.96 5.25733 2 ;O3'- P- O5'- C5' 28 29
32 33 1 357.25 1.48473 3 ;O3'- P- O5'- C5'
So, this would only work if funct was 9 and not 1 as above? The way it is, the
last line of a sequence dih. is overwriting the 2 previous one, ignoring them
completely?
From src/gmxlib/{ifunc,bondfree}.c and src/kernel/{topdirs,toppush}.c it can
be seen that dihedraltypes 4 and 1 call the same evaluation function. Perhaps
Erik can confirm this.
src/gmxlib/ifunc.c did suggest to me that something is not quite right...
def_bonded (PDIHS,Proper Dih., 4, 3, 3, eNR_PROPER, pdihs
),
def_bonded (RBDIHS, Ryckaert-Bell., 4, 6, 6, eNR_RB, rbdihs
),
def_bonded (FOURDIHS, Fourier Dih.,4, 4, 4, eNR_FOURDIH, rbdihs
[gmx-users] RE: Targeted MD
Hello, I realize that this topic has been discussed before, but I just need to ascertain a few things: I have a system of about 1400 atoms with implicit solvent and I want to do a targeted MD. While doing the pre-processing, if I just specify grompp -r in.gro -rb out.gro, is this sufficient or are there any other things that I need to consider. Also, I have tabulated potentials. If any one knows how to do this, or if you need more info on my system, please let me know. Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] force constants for umbrellla histograms
Hi all Is is O.K to use different force constants for different sampling windows for the generation of the potential of mean force curves? Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: Targeted MD
Hi, -r and -rb are for FEP. If you want to bias your simulation's sampling, you can use the pull code, essential dynamics sampling or flooding, all of which are described in the manual and literature. Ran Nimesh Jain wrote: Hello, I realize that this topic has been discussed before, but I just need to ascertain a few things: I have a system of about 1400 atoms with implicit solvent and I want to do a targeted MD. While doing the pre-processing, if I just specify grompp -r in.gro -rb out.gro, is this sufficient or are there any other things that I need to consider. Also, I have tabulated potentials. If any one knows how to do this, or if you need more info on my system, please let me know. Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] How to center molecules in the box with trjconj ?
Hi all, I have simulated a system containing 55 DPC molecules, a peptide some ions and water in a cubic box. Initially all molecules were placed randomly in the box. As expected during the simulation all the DPC molecules aggregate to form a stable micelle with the peptide located at the micelle interface. Now I would like to plot some MD configs in a PDB format some configs where the micelle and the peptide are placed in the center of the box. To take into account the PBC and to obtain the PDB, for the last frame at 150 ns as I used trjconv with the following commands: 1- trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump -b 15 -e 15 -o traj_KTM17_DPC_0ns_noJump.pdb With non-SOL (DPC and peptide) as a group for output and where traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation 2- trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro -center -o traj_KTM17_DPC_0ns_noJump_center.pdb With DPC as a group for centering and System (DPC and peptide) as a group for output. the *.gro file contains only the DPC and peptide. Unfortunately, these commands do not work since the micelle (and the peptide) are not in the box center. I have tried many others commands with -pbc as mol, res with no success. I used GMX version 4.0.7 Any advices would be helpful. Stefane -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force constants for umbrellla histograms
On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote: Hi all Is is O.K to use different force constants for different sampling windows for the generation of the potential of mean force curves? Yes. Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber
Ah! now I get it. Thanks Berk. On 20 August 2010 16:27, gmx-users-requ...@gromacs.org wrote: Hi, That depends. If you have explicit parameters in the dihedral section then 1 and 9 are equivalent. If grompp has to look up parameters in the dihderaltypes section there will be difference when multiple parameter lines are present the same atom types for a dihedral type 9. Berk -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] intersting problem
dear all I want to calculate the how many water molecule are their with in 3.5 A of a particular atom. could anyone help me in this regard E R Azhagiya singam -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force constants for umbrellla histograms
Thanks Xavier Then does it matter how many times you vary it, and how large ? In my sampling I have very good histograms up to 2 nm (force constant = 1000 kj/mol), above 2nm they are not. I feel I may have to use a force constant of 500 for the next 3 or 4 windows, and even less again (ca~ 50 kj/mol) beyond that. Cheers Gavin XAvier Periole wrote: On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote: Hi all Is is O.K to use different force constants for different sampling windows for the generation of the potential of mean force curves? Yes. Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to center molecules in the box with trjconj ?
ABEL Stephane 175950 wrote: Hi all, I have simulated a system containing 55 DPC molecules, a peptide some ions and water in a cubic box. Initially all molecules were placed randomly in the box. As expected during the simulation all the DPC molecules aggregate to form a stable micelle with the peptide located at the micelle interface. Now I would like to plot some MD configs in a PDB format some configs where the micelle and the peptide are placed in the center of the box. To take into account the PBC and to obtain the PDB, for the last frame at 150 ns as I used trjconv with the following commands: 1- trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump -b 15 -e 15 -o traj_KTM17_DPC_0ns_noJump.pdb With non-SOL (DPC and peptide) as a group for output and where traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation 2- trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro -center -o traj_KTM17_DPC_0ns_noJump_center.pdb With DPC as a group for centering and System (DPC and peptide) as a group for output. the *.gro file contains only the DPC and peptide. Unfortunately, these commands do not work since the micelle (and the peptide) are not in the box center. I have tried many others commands with -pbc as mol, res with no success. I have never had much success using multi-molecule groups for centering or other correction using trjconv. Centering on the peptide, i.e. trjconv -pbc mol -ur compact -center, should do the trick. I have never found -pbc nojump to work very well, for a reason that is still unknown to me. -Justin I used GMX version 4.0.7 Any advices would be helpful. Stefane -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] intersting problem
babu gokul wrote: dear all I want to calculate the how many water molecule are their with in 3.5 A of a particular atom. could anyone help me in this regard g_dist -dist -Justin E R Azhagiya singam -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] force constants for umbrellla histograms
The most important is that you have to put in trajectories that are equilibrated! You can mix as much force constant values you like but always equilibrated ... Then the lower the force constant the longer the simulation needs to be to reach equilibrium: larger conformational space accessible. I can also imagine that a too strong force constant might deform your molecules in a manner you should not. Then does it matter how many times you vary it, and how large ? In my sampling I have very good histograms up to 2 nm (force constant = 1000 kj/mol), above 2nm they are not. I feel I may have to use a force constant of 500 for the next 3 or 4 windows, and even less again (ca~ 50 kj/mol) beyond that. Cheers Gavin XAvier Periole wrote: On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote: Hi all Is is O.K to use different force constants for different sampling windows for the generation of the potential of mean force curves? Yes. Many Thanks Gavin -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
