[gmx-users] Visualization of .trr problem in VMD
Dear All I am working on protein unfolding simulation in gromacs. when I do a production run on 32 node HPC I get .trr file along with .gro. when I try to visualize this files in VMD I see erratic large movement of atoms in the trajectory. With same .mdp files when I did smaller run of 2ns on single PC and viewed .trr and .gro in VMD, the movemnt of atom was smooth. Why this is happening. When I used the command g_filter to produce lowpass.xtc with -nf 10 I got the smooth movement of atoms. Is it always essential to use g_filter with .trr file of HPC multinode output. what is the difference between lowpass.xtc and highpass.xtc. For the pupose of RMSD calculation should I use the output of g_filter i.e. lowpass.xtc or the original .trr file. I am new in this field so excuse me for some basic mistakes . Any suggestion and help will highly appreciated. Thanking you in advance. msnayeem msnay...@gmail.com -- 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] Can gromacs be compiled for openmp
Hi everyone, Can gromacs be compiled for openmp Due to use mulitcore processors, so I am interested in how to compile with openmp. Thanks and regards, lina -- 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] Visualization of .trr problem in VMD
shahid nayeem wrote: Dear All I am working on protein unfolding simulation in gromacs. when I do a production run on 32 node HPC I get .trr file along with .gro. when I try to visualize this files in VMD I see erratic large movement of atoms in the trajectory. With same .mdp files when I did smaller run of 2ns on single PC and viewed .trr and .gro in VMD, the movemnt of atom was smooth. Why this is happening. When I used the command g_filter to produce lowpass.xtc This sounds like a consequence of periodic boundary conditions. Have you tried using trjconv to fix the PBC effects (i.e., -pbc mol, -pbc nojump, or something similar)? with -nf 10 I got the smooth movement of atoms. Is it always essential to use g_filter with .trr file of HPC multinode output. what is the difference between lowpass.xtc and highpass.xtc. For the pupose of The purpose is to smooth out high-frequency vibration to make visualization a bit easier and movie-rendering more meaningful. See g_filter -h for the difference between the two; they are explained quite thoroughly. RMSD calculation should I use the output of g_filter i.e. lowpass.xtc or the original .trr file. I am new in this field so excuse me for Use the original (PBC-corrected) trajectory. -Justin some basic mistakes . Any suggestion and help will highly appreciated. Thanking you in advance. msnayeem msnay...@gmail.com -- 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] Can gromacs be compiled for openmp
On 4/3/10 1:08 PM, lina wrote: Hi everyone, Can gromacs be compiled for openmp Due to use mulitcore processors, so I am interested in how to compile with openmp. Thanks and regards, lina There is no openmp implementation of mdrun in gromacs. The upcoming version 4.5 will have a threaded implementation though, but for now you need to compile with MPI. -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://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] Re: gmx-users Digest, Vol 72, Issue 13
Hi,
I tried to use 4 and 8 CPUs.
There are about 6000 atoms in my system.
The interconnect of our computer is the network with speed 1Gb but not optical
fiber.
I'm sorry for my poor English and I couldn't express well in my question.
Everytime I submitted the parallel job, the nodes assigned to mehave been 100%
loading,
and the CPU source availble to me is less then 10%.
I think there is something wrong with my submit script or executable script,
so I post them in my question before.(please see those below)
Hsin-Lin
Hi,
how many CPUs do you try to use? How big is your system. What kind of
interconnect? Since you use condor probably some pretty slow interconnect.
Than you can't aspect it to work on many CPUs. If you want to use many CPUs
for MD you need a faster interconnect.
Roland
2010/4/2 Hsin-Lin Chiang jian...@phys.sinica.edu.tw
#160;Hi,
Do someone use gromacs, lam, and condor together here?
I use gromacs with lam/mpi on condor system.
Everytime I submit the parallel job.
I got the node which is occupied before and the performance of each cpu is
below 10%.
How should I change the script?
Below is one submit script and two executable script.
condor_mpi:
#!/bin/bash
Universe = parallel
Executable = ./lamscript
machine_count = 2
output = md_$(NODE).out
error = md_$(NODE).err
log = md.log
arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh
+WantIOProxy = True
should_transfer_files = yes
when_to_transfer_output = on_exit
Queue
---
lamscript:
---
#!/bin/sh
_CONDOR_PROCNO=$_CONDOR_PROCNO
_CONDOR_NPROCS=$_CONDOR_NPROCS
_CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR
SSHD_SH=`condor_config_val libexec`
SSHD_SH=$SSHD_SH/sshd.sh
CONDOR_SSH=`condor_config_val libexec`
CONDOR_SSH=$CONDOR_SSH/condor_ssh
# Set this to the bin directory of your lam installation
# This also must be in your .cshrc file, so the remote side
# can find it!
export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4
export PATH=${LAMDIR}/bin:${PATH}
export LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib
. $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS
# If not the head node, just sleep forever, to let the
# sshds run
if [ $_CONDOR_PROCNO -ne 0 ]
then
#160; #160; #160; #160; #160; #160; #160; #160; wait
#160; #160; #160; #160; #160; #160; #160; #160; sshd_cleanup
#160; #160; #160; #160; #160; #160; #160; #160; exit 0
fi
EXECUTABLE=$1
shift
# the binary is copied but the executable flag is cleared.
# so the script have to take care of this
chmod +x $EXECUTABLE
# to allow multiple lam jobs running on a single machine,
# we have to give somewhat unique value
export LAM_MPI_SESSION_SUFFIX=$$
export LAMRSH=$CONDOR_SSH
# when a job is killed by the user, this script will get sigterm
# This script have to catch it and do the cleaning for the
# lam environment
finalize()
{
sshd_cleanup
lamhalt
exit
}
trap finalize TERM
CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact
export $CONDOR_CONTACT_FILE
# The second field in the contact file is the machine name
# that condor_ssh knows how to use. Note that this used to
# say sort -n +0 ..., but -n option is now deprecated.
sort $CONDOR_CONTACT_FILE | awk '{print $2}' machines
# start the lam environment
# For older versions of lam you may need to remove the -ssi boot rsh line
lamboot -ssi boot rsh -ssi rsh_agent $LAMRSH -x machines
if [ $? -ne 0 ]
then
#160; #160; #160; #160; echo lamscript error booting lam
#160; #160; #160; #160; exit 1
fi
mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@
CHILD=$!
TMP=130
while [ $TMP -gt 128 ] ; do
#160; #160; #160; #160; wait $CHILD
#160; #160; #160; #160; TMP=$?;
done
# clean up files
sshd_cleanup
/bin/rm -f machines
# clean up lam
lamhalt
exit $TMP
md.sh
#!/bin/sh
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
-s /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.tpr \
-e /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.edr \
-o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \
-g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \
-c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro
-
Hsin-Lin
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[gmx-users] g_sas
Hi The command g_sas = Select a group for calculation of surface and a group for output What is the difference between a group for calculation of surface and a group for output? Thank you Lin -- 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] g_sas
Chih-Ying Lin wrote: Hi The command g_sas = Select a group for calculation of surface and a group for output What is the difference between a group for calculation of surface and a group for output? Please consult the documentation. From g_sas -h: The program will ask for a group for the surface calculation and a group for the output. The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. -Justin Thank you Lin -- 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] g_sas
On 4/3/10 8:36 PM, Justin A. Lemkul wrote: Chih-Ying Lin wrote: Hi The command g_sas = Select a group for calculation of surface and a group for output What is the difference between a group for calculation of surface and a group for output? Please consult the documentation. From g_sas -h: The program will ask for a group for the surface calculation and a group for the output. The calculation group should always consists of all the non-solvent atoms in the system. The output group can be the whole or part of the calculation group. Actually this documentation is not correct. The calculation group are those atoms taken into account in the computation, whether or not they are solvent accessible. If you select a group consisting of a single residue in a protein the SAS will be computed as if the rest of the protein is not there. Very useful when you want to compute protein-protein interface areas. -Justin Thank you Lin -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://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
Re: [gmx-users] DSSP = how to edit .eps file
Chih-Ying Lin wrote: HI After running DSSP, .eps files are created. No they aren't; you create .eps files from the .xpm output that do_dssp generates. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues. How can i do it? As with most (all) Gromacs analysis tools, create an index group for the residues you want to analyze. That will require you to re-run your analysis or otherwise hack your .xpm file (probably not a good idea). Also, how can I change the thickness of the color band for each residue? Use an appropriate .m2p file to alter the attributes of the data. An example is given in the online manual. The logo indicates the color of different second structure is shown not clear for me, how can i make the change on it? Do you want to change the colors assigned, or some other aspect of the legend? You could, in theory, edit the color assignments in the .xpm file. -Justin Thank you Lin -- 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] DSSP = how to edit .eps file
On 4/3/10 9:19 PM, Justin A. Lemkul wrote: Chih-Ying Lin wrote: HI After running DSSP, .eps files are created. No they aren't; you create .eps files from the .xpm output that do_dssp generates. We can see the second structures of the all residues. I only want to see the change of the second structures of some specific residues. How can i do it? As with most (all) Gromacs analysis tools, create an index group for the residues you want to analyze. That will require you to re-run your analysis or otherwise hack your .xpm file (probably not a good idea). Also, how can I change the thickness of the color band for each residue? Use an appropriate .m2p file to alter the attributes of the data. An example is given in the online manual. The logo indicates the color of different second structure is shown not clear for me, how can i make the change on it? Do you want to change the colors assigned, or some other aspect of the legend? You could, in theory, edit the color assignments in the .xpm file. With the option -sss string HE you can also choose to show only helix and sheet -Justin Thank you Lin -- David. David van der Spoel, PhD, Professor of Biology Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://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
Re: [gmx-users] Re: gmx-users Digest, Vol 72, Issue 13
On 4/04/2010 3:13 AM, Hsin-Lin Chiang wrote:
Hi,
I tried to use 4 and 8 CPUs.
There are about 6000 atoms in my system.
The interconnect of our computer is the network with speed 1Gb but not
optical fiber.
Gigabit ethernet is too slow for good scaling of GROMACS beyond about 2
or 4 cpus.
I'm sorry for my poor English and I couldn't express well in my question.
Everytime I submitted the parallel job, the nodes assigned to me have
been 100% loading,
and the CPU source availble to me is less then 10%.
I think there is something wrong with my submit script or executable
script,
so I post them in my question before.(please see those below)
You're apparently using double-precision GROMACS. That makes everything,
including communication, much slower. Consider not doing that.
Mark
Hsin-Lin
Hi,
how many CPUs do you try to use? How big is your system. What kind of
interconnect? Since you use condor probably some pretty slow
interconnect.
Than you can't aspect it to work on many CPUs. If you want to use
many CPUs
for MD you need a faster interconnect.
Roland
2010/4/2 Hsin-Lin Chiang jian...@phys.sinica.edu.tw
Hi,
Do someone use gromacs, lam, and condor together here?
I use gromacs with lam/mpi on condor system.
Everytime I submit the parallel job.
I got the node which is occupied before and the performance of each
cpu is
below 10%.
How should I change the script?
Below is one submit script and two executable script.
condor_mpi:
#!/bin/bash
Universe = parallel
Executable = ./lamscript
machine_count = 2
output = md_$(NODE).out
error = md_$(NODE).err
log = md.log
arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh
+WantIOProxy = True
should_transfer_files = yes
when_to_transfer_output = on_exit
Queue
---
lamscript:
---
#!/bin/sh
_CONDOR_PROCNO=$_CONDOR_PROCNO
_CONDOR_NPROCS=$_CONDOR_NPROCS
_CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR
SSHD_SH=`condor_config_val libexec`
SSHD_SH=$SSHD_SH/sshd.sh
CONDOR_SSH=`condor_config_val libexec`
CONDOR_SSH=$CONDOR_SSH/condor_ssh
# Set this to the bin directory of your lam installation
# This also must be in your .cshrc file, so the remote side
# can find it!
export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4
export PATH=${LAMDIR}/bin:${PATH}
export
LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib
. $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS
# If not the head node, just sleep forever, to let the
# sshds run
if [ $_CONDOR_PROCNO -ne 0 ]
then
wait
sshd_cleanup
exit 0
fi
EXECUTABLE=$1
shift
# the binary is copied but the executable flag is cleared.
# so the script have to take care of this
chmod +x $EXECUTABLE
# to allow multiple lam jobs running on a single machine,
# we have to give somewhat unique value
export LAM_MPI_SESSION_SUFFIX=$$
export LAMRSH=$CONDOR_SSH
# when a job is killed by the user, this script will get sigterm
# This script have to catch it and do the cleaning for the
# lam environment
finalize()
{
sshd_cleanup
lamhalt
exit
}
trap finalize TERM
CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact
export $CONDOR_CONTACT_FILE
# The second field in the contact file is the machine name
# that condor_ssh knows how to use. Note that this used to
# say sort -n +0 ..., but -n option is now deprecated.
sort $CONDOR_CONTACT_FILE | awk '{print $2}' machines
# start the lam environment
# For older versions of lam you may need to remove the -ssi boot
rsh line
lamboot -ssi boot rsh -ssi rsh_agent $LAMRSH -x machines
if [ $? -ne 0 ]
then
echo lamscript error booting lam
exit 1
fi
mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@
CHILD=$!
TMP=130
while [ $TMP -gt 128 ] ; do
wait $CHILD
TMP=$?;
done
# clean up files
sshd_cleanup
/bin/rm -f machines
# clean up lam
lamhalt
exit $TMP
md.sh
#!/bin/sh
#running GROMACS
/stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
-s /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.tpr \
-e /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.edr \
-o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \
-g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \
-c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro
-
Hsin-Lin
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[gmx-users] Potential Tables for user defined potentials
Hi I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions. So my question is that, how can I use potential table approach to specify fluid-fluid and fluid-wall interactions seperately? Thanks sikandar -- 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] Potential Tables for user defined potentials
Sikandar Mashayak wrote: Hi I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that I need to use custom potential field parameters for fluid-fluid and fluid-wall interactions. So my question is that, how can I use potential table approach to specify fluid-fluid and fluid-wall interactions seperately? Start with the manual, section 6.7.2, and see the table*.xvg in the /share/top subdirectory of your Gromacs installation for examples. -Justin Thanks sikandar -- 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: insert silicon atoms into ice structure
Thanks for reply. I intended to add these silicon atoms into ice structure, the Santan William wrote: Dear GMXusers, I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot. If zero atoms were inserted, there probably isn't enough space for them in the box. -Justin Best, william -- 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: insert silicon atoms into ice structure (Justin A. Lemkul)
Thanks for reply. I intended to add some silicon atoms just into ice structure, so the simulation box only containing ice. You said there probably isn't enough space for them in the box. Did you mean I can't insert these atoms into ice structure if the box only containing ice? Is there any other way to insert silicon atoms into a solid ice structure? Thanks a lot. Best, william Santan William wrote: Dear GMXusers, I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot. If zero atoms were inserted, there probably isn't enough space for them in the box. -Justin Best, william -- 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: insert silicon atoms into ice structure (Justin A. Lemkul)
Santan William wrote: Thanks for reply. I intended to add some silicon atoms just into ice structure, so the simulation box only containing ice. You said there probably isn't enough space for them in the box. Did you mean I can't insert these atoms into ice structure if the box only containing ice? Well, are there cavities in the ice structure sufficiently large to fit your silicon atoms? Judging by the failure of your approach, I'd say there's not. Is there any other way to insert silicon atoms into a solid ice structure? You could try generating some random configuration of silicon atoms, then: genbox -cp si.pdb -cs ice.pdb You would then, of course, be potentially interrupting the lattice of water molecules if some are deleted due to overlap with your silicon atoms. But as for whether or not that's important, you'll have to decide. -Justin Thanks a lot. Best, william Santan William wrote: Dear GMXusers, I wanna insert several silicon atoms into an ice crystal. I use genbox with a Silicon.pdb, but there's no any silicon atom in the out file. Do I miss anything? Anyone has some comments? Thanks a lot. If zero atoms were inserted, there probably isn't enough space for them in the box. -Justin Best, william -- 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] DSSP= how to edit .eps file
HI 1. dssp -n index.ndx = only atom numbers of one residue in the index.ndx = can dssp decide the exact second structure for the only one residue without considering other residues of protein? = can i get the same second structure for the residue with [ dssp -n one-residue.ndx ] and [dssp -n protein-main chain + H .ndx ] ? 2. The legend indicates the color of different second structure is shown under the secondary-structure plot. I don't want to change the colors assigned, but one legend is half-shown. The picture of legend is cut. How can I get that legend full-shown. 3. With the option -sss string HE HE = helix ? Thanks Lin -- 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_sas
HI THe command = g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg In the solvent-accessible-surface.xvg = @ s0 legend Hydrophobic @ s1 legend Hydrophilic @ s2 legend Total @ s3 legend D Gsolv What does Hydrophobic mean here? What does Hydrophilic mean here? Does Total = Hydrophobic+Hydrophilic ? What does D Gsolv mean here? How can Gromacs define Hydrophobic atoms and Hydrophilic atoms ? What does the Area unit mean ? = Area (nm\S2\N) Thank you Lin -- 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
