Re: [gmx-users] error group protein not found
Hi, if there is a protein in your system you should have protein as standard group. Maybe you use a template mdp file in which the temperature coupling group is protein. if you have no protein in your simulation check the mdp files for tc-grps and adjust accordingly. Max On Jun 3, 2015, at 3:07 PM, Victor Rosas Garcia rosas.vic...@gmail.com wrote: Hello, In your command line you do not specify an index file. Maybe you need to generate one. Check out usage of make_ndx. Hope this helps Victor 2015-06-03 13:41 GMT-05:00 marzieh dehghan dehghanmarz...@gmail.com: Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. please let me know how can I solve this problem. I am looking forward to getting your answer thanks a lot -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error group protein not found
Hello, In your command line you do not specify an index file. Maybe you need to generate one. Check out usage of make_ndx. Hope this helps Victor 2015-06-03 13:41 GMT-05:00 marzieh dehghan dehghanmarz...@gmail.com: Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. please let me know how can I solve this problem. I am looking forward to getting your answer thanks a lot -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] fix COM of a group
Dear Tsjerk, Yes, you are right. I want to fix the COM of the reference group (one end of a triple helix), and pull the other end. I tried to freeze the reference group, but found this setting restricted the unfolding process of my triple helix. That's why I want to find a way to fix the COM only. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 11:18 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, You didn't tell you were pulling... That's a totally different matter. I guess you want to use two pull groups and pull one with respect to the other. Cheers, Tsjerk On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Tsjerk, Thanks for your guidance. I add those two command lines you gave in .mdp, but got the following warnings. WARNING 1 [file dynamic.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. Number of degrees of freedom in T-Coupling group Protein is 8680.88 Number of degrees of freedom in T-Coupling group non-Protein is 202734.12 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm WARNING 2 [file dynamic.mdp]: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 3 1919 -1.542 nm -1.542 nm Can I just ignore them? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 5:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations
i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings in my production mdp file : Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 ms dt = 0.002 ; 2 fs ; Output control ;trr file nstxout = 50; save coordinates every 1ns nstvout = 50; save velocities every 1ns nstenergy = 1 ; save energies every 20ps nstlog = 1 ; update log file every 20ps ;xtc file nstxtcout = 1 ; xtc compressed trajectory output every 20 ps ; Bond parameters constraint_algorithm = LINCS; holonomic constraints constraints= none ;ns-type= simple nstlist = 0 rlist = 0 coulombtype = Cut-off rcoulomb= 0.0 rvdw= 0 Periodic boundary conditions pbc = no; 3-D PBC ; Velocity generation gen_vel = YES ; Velocity generation is on comm_mode = ANGULAR however i get LINCS warning and also the log file says this : Your simulation settings would have triggered the efficient all-vs-all kernels in GROMACS 4.5, but these have not been implemented in GROMACS 4.6. Also, we can't use the accelerated SIMD kernels here because of an unfixed bug. The reference C kernels are correct, though, so we are proceeding by disabling all CPU architecture-specific (e.g. SSE2/SSE4/AVX) routines. If performance is important, please use GROMACS 4.5.7 or try cutoff-scheme = Verlet. kindly suggest something .. -- Best *,* Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] temperature problem
On 6/3/15 3:46 AM, Lovika Moudgil wrote:
Hi...thanks for reply Peter and Mark I tried with temperature coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Using a plain cutoff in the condensed phase is outdated methodology that is very
inaccurate. Cutoff artifacts lead to accumulation of heat in the system. Use
something sensible like PME.
-Justin
Thanks and Regards
Lovika
On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Runaway heating is the only useful feature of cutoff electrostatics. Use an
actual model physics.
Mark
On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon p.c.kr...@rug.nl wrote:
On 02/06/15 09:43, Lovika Moudgil wrote:
Hi everyone
I am having some problem in my md run .In my system temperature of
system
is abruptly increasing .I have done nvt for 50 picoseconds ..nd then
using
it for further md simulation .I am not getting any error for this
temperature increase .But when I plot temperature graph ,
temperature
is not same as nvt and is very high in md .I am having gold slab and
amino
acid in my system . Mdp file for md run is below Is their any error
in
my mdp file ???what could be the reason for this ???Please suggest
; Run parameters
integrator= md; leap-frog integrator
nsteps= 3000; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write
coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc
trajectory
energygrps = System; group(s) to write to energy
file
; Bond parameters
constraint_algorithm= lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy
atom-H bonds) constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen
thermostat
tc-grps= Protein AUS AUB AUI SOL NA CL; two coupling
groups -
more accurate
tau_t= 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant,
in ps
ref_t= 300 300 300 300 300 300 300; reference
temperature, one for each group, in K
You have too many temperature coupling groups. (What Not To Do on
http://www.gromacs.org/Documentation/Terminology/Thermostats)
I'd stick to one for proteins, and one for the rest.
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
; Velocity generation
gen_vel= yes; assign velocities from Maxwell
distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
comm_mode= None
Thanks and Reagrds
Lovika
Peter
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==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Re: [gmx-users] No default Ryckaert-Bell. types for proline
On 6/3/15 12:00 AM, Kevin C Chan wrote: Thanks Justin, I have long been confused by atom names and types in Gromacs topology. I have just went through the manual again, and it confirms me that what we read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are atomtypes. In other words, what you have listed in the last email C CT_2 N CT_33 -5.72371 -18.33847 -5.23419 29.29636 0.0 0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97 C CT_2 NT CT_33 -5.72371 -18.33847 -5.23419 29.29636 0.0 0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97 C_3CT_2 N CT_33 -5.72371 -18.33847 -5.23419 29.29636 0.0 0.0 ; Pro COO- terminus. C_3CT_2 NT CT_33 -5.72371 -18.33847 -5.23419 29.29636 0.0 0.0 ; Pro COO- terminus. which was extracted from ffbonded.itp is composed of atomtypes. Meanwhile what I have stated in the brackets - (CD N CA C), (CD N CA CB) or (CD N CA HA) are by myself read from the topology file after pdb2gmx. To be exact, I read [ dihedrals ] ; aiajakal functc0c1c2 c3c4c5 12 1 4 5 3 12 1 4 6 3 12 1 415 3 from the topology and refer the numbers (e.g. 12 1 4 15) to the above directive [ atoms ] to find out that it is (CD N CA C). We can also read from directive [ atoms ] that under the type column, it should be (opls_296 opls_309 opls_285 opls_271). So which is the atomtypes, (CD N CA C) or (opls_296 opls_309 opls_285 opls_271)? It seems (opls_296 opls_309 opls_285 opls_271) are the atomtypes, but why the itp states (C CT_2 N CT_3)? And how can I refer my topology to this line of parameter when it deals (CD N CA C) or (opls_296 opls_309 opls_285 opls_271)? Refer to ffnonbonded.itp. The first column (ignore the fact that it says name as it is actually a type) is the opls_* atom type for nonbonded interactions, the second column is the translated bonded type. There are fewer bonded types (less diversity in interactions) and this convention removes the need for tons of redundant parameters. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Hi, I'm not accustomed with coarse grained, but from the little stuff I know on MD in order to keep a box's size constant you have to use an NVT simulation not an NPT. Meaning don't keep pressure constant but rather the volume. Do double check though, I might be wrong. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of HongTham hongtham0...@gmail.com Sent: Friday, May 29, 2015 9:13 AM To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Dear Gromacs User, I simulated a coarse grained membrane protein system. This is my pressure control parameter. ; pressure control Pcoupl = berendsen ; Pcoupltype = semiisotropic ; tau-p= 5.0 5.0 ; compressibility = 4.5e-5 4.5e-5 ; ref-p= 1.0 1.0 1.0 1.0 ; refcoord_scaling = all ; Although I set Pcoupltype as semiisotropic, after running simulation a while, my box was changed from cubic (starting) to rectangular parallelepiped. the x,y direction were shortened while z direction was lengthened a lot. is there any option to control the box size through the simulation? Thank you so much. Hongtham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Center of mass motion removal
Hi Tsjerk, So what different between nstcomm nsteps case and comm-mode = none case? Because when I set this option (comm-mode = none), the dynamisc tpr file can not be run. It returned the error related to built up the kinetics energy. But it didn't with nstcomm nsteps, the md still be performed. Cheer, Hongtham On Wed, Jun 3, 2015 at 3:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Tuong Vy, Right. If COMM is removed every N steps and the simulation runs for M N steps, then COMM will never actually be removed. Cheers, Tsjerk On Jun 3, 2015 4:44 AM, Vy Phan phanvy120...@gmail.com wrote: Dear all, I wonder when I set the comm-mode =Linear , and nstcomm (frequency for COM motion removal) nststeps (maxinum number of steps), the MD simulation can be performed. I think the nstcomm nsteps mean COM motion is not removed (the MD simulation can be not performed) Could somebody explain to me ? Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Center of mass motion removal
Dear Tsjerk.
I see. Many thanks your explanation.
Tuong Vy
2015-06-03 15:44 GMT+09:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi Tuong Vy,
There is no difference in practice except for raising the error. The
developers can't try catching all possible foolish things people could try
with an error. Also, if you think of fooling the program in this way, you
may be assumed to know what you're doing (and why you wouldn't need to
worry about flying ice cubes).
Cheers,
Tsjerk
On Jun 3, 2015 8:23 AM, Vy Phan phanvy120...@gmail.com wrote:
Dear Tsjerk and all,
If I set up the comm-mode =None ( COM motion is not removed), i got the
Warning : numerical rounding errors can lead to build up of kinetic
energy
of the COM and the simulation can not run.
I think comm-mode =None and {comm-mode =Linear , nstcomm nststeps) is
similar meaning.
I misunderstand something?
Could you explain more?
Many Thanks
Tuong Vy
2015-06-03 15:11 GMT+09:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi Tuong Vy,
Right. If COMM is removed every N steps and the simulation runs for M
N
steps, then COMM will never actually be removed.
Cheers,
Tsjerk
On Jun 3, 2015 4:44 AM, Vy Phan phanvy120...@gmail.com wrote:
Dear all,
I wonder when I set the comm-mode =Linear , and nstcomm
(frequency for COM motion removal) nststeps (maxinum number of
steps),
the MD simulation can be performed.
I think the nstcomm nsteps mean COM motion is not removed (the MD
simulation can be not performed)
Could somebody explain to me ?
Tuong Vy
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Re: [gmx-users] temperature problem
Hi...thanks for reply Peter and Mark I tried with temperature coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Thanks and Regards
Lovika
On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Runaway heating is the only useful feature of cutoff electrostatics. Use an
actual model physics.
Mark
On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon p.c.kr...@rug.nl wrote:
On 02/06/15 09:43, Lovika Moudgil wrote:
Hi everyone
I am having some problem in my md run .In my system temperature of
system
is abruptly increasing .I have done nvt for 50 picoseconds ..nd then
using
it for further md simulation .I am not getting any error for this
temperature increase .But when I plot temperature graph ,
temperature
is not same as nvt and is very high in md .I am having gold slab and
amino
acid in my system . Mdp file for md run is below Is their any error
in
my mdp file ???what could be the reason for this ???Please suggest
; Run parameters
integrator= md; leap-frog integrator
nsteps= 3000; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write
coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc
trajectory
energygrps = System; group(s) to write to energy
file
; Bond parameters
constraint_algorithm= lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy
atom-H bonds) constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen
thermostat
tc-grps= Protein AUS AUB AUI SOL NA CL; two coupling
groups -
more accurate
tau_t= 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant,
in ps
ref_t= 300 300 300 300 300 300 300; reference
temperature, one for each group, in K
You have too many temperature coupling groups. (What Not To Do on
http://www.gromacs.org/Documentation/Terminology/Thermostats)
I'd stick to one for proteins, and one for the rest.
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
; Velocity generation
gen_vel= yes; assign velocities from Maxwell
distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
comm_mode= None
Thanks and Reagrds
Lovika
Peter
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Re: [gmx-users] temperature problem
Hi, reconstruct both the .mdp (NVT, Md) files as follows- tc_groups = Protein Non-protein tau_t =0.1 0.1 ref_t =300 300 This should work. Soumadwip -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Center of mass motion removal
Hi Tuong Vy,
There is no difference in practice except for raising the error. The
developers can't try catching all possible foolish things people could try
with an error. Also, if you think of fooling the program in this way, you
may be assumed to know what you're doing (and why you wouldn't need to
worry about flying ice cubes).
Cheers,
Tsjerk
On Jun 3, 2015 8:23 AM, Vy Phan phanvy120...@gmail.com wrote:
Dear Tsjerk and all,
If I set up the comm-mode =None ( COM motion is not removed), i got the
Warning : numerical rounding errors can lead to build up of kinetic energy
of the COM and the simulation can not run.
I think comm-mode =None and {comm-mode =Linear , nstcomm nststeps) is
similar meaning.
I misunderstand something?
Could you explain more?
Many Thanks
Tuong Vy
2015-06-03 15:11 GMT+09:00 Tsjerk Wassenaar tsje...@gmail.com:
Hi Tuong Vy,
Right. If COMM is removed every N steps and the simulation runs for M N
steps, then COMM will never actually be removed.
Cheers,
Tsjerk
On Jun 3, 2015 4:44 AM, Vy Phan phanvy120...@gmail.com wrote:
Dear all,
I wonder when I set the comm-mode =Linear , and nstcomm
(frequency for COM motion removal) nststeps (maxinum number of
steps),
the MD simulation can be performed.
I think the nstcomm nsteps mean COM motion is not removed (the MD
simulation can be not performed)
Could somebody explain to me ?
Tuong Vy
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Re: [gmx-users] fix COM of a group
Dear Tsjerk, Thanks for your guidance. I add those two command lines you gave in .mdp, but got the following warnings. WARNING 1 [file dynamic.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. Number of degrees of freedom in T-Coupling group Protein is 8680.88 Number of degrees of freedom in T-Coupling group non-Protein is 202734.12 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm WARNING 2 [file dynamic.mdp]: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 3 1919 -1.542 nm -1.542 nm Can I just ignore them? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 5:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Volume of active site
Dear Erik, As per your suggestion I have tried gmx sasa -tv option to get the volume of the active site with help of a defined set of residues (17 residues) as defined in the index file. But for all systems, mutants and wild type enzymes have similar profile of volume throughout the simulation time of 10ns and all volume shows up 6 nm3 as center point but visualization has shown widening of active site in the simulation. Is it the right approach to get the volume of the defined cavity or something like may I have to remove the bound substrate from the trajectory or some other thing I have to take care of while using the tool... I am just wonder what you had mentioned as clever use of the tool gmx sasa ? Could you please little more explicit in the usage of the tool for volume prediction . Regards, Raja On Jun 1, 2015 8:42 PM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Raja, Depending on how you define that volume, you may achieve what you want through clever use of g_sas -tv (gmx sas nowadays). Kind regards, Erik On 1 Jun 2015, at 15:19, Raj D gromacs.fo...@gmail.com wrote: Dear user, I have completed a set of MD simulations of mutants and wild type of a protein complexed with its substrate in its active site , I have inferred that the active sites of all mutant enzymes have gone enlarged relative to wild type which is consistent with our kinetic study of the mutants, the Km values are so high for all mutant enzymes and I would like quantify the volume of the active site comprising a set of 17 active site residues ..Is there any direct or indirect tool in gromacs to compute the volume like that ? Or any free tools available . Regards, Raja -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] fix COM of a group
Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Center of mass motion removal
Hi Tuong Vy, Right. If COMM is removed every N steps and the simulation runs for M N steps, then COMM will never actually be removed. Cheers, Tsjerk On Jun 3, 2015 4:44 AM, Vy Phan phanvy120...@gmail.com wrote: Dear all, I wonder when I set the comm-mode =Linear , and nstcomm (frequency for COM motion removal) nststeps (maxinum number of steps), the MD simulation can be performed. I think the nstcomm nsteps mean COM motion is not removed (the MD simulation can be not performed) Could somebody explain to me ? Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] fix COM of a group
Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Hi, If you want to preserve the cubic shape of your box you need to choose a barostat that allows to use the isotropic option. However, when using a barostat your box size is going to change for sure. Cheers, Mario 2015-06-03 10:06 GMT+02:00 Sotirios Dionysios I. Papadatos si.papada...@edu.cut.ac.cy: Hi, I'm not accustomed with coarse grained, but from the little stuff I know on MD in order to keep a box's size constant you have to use an NVT simulation not an NPT. Meaning don't keep pressure constant but rather the volume. Do double check though, I might be wrong. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of HongTham hongtham0...@gmail.com Sent: Friday, May 29, 2015 9:13 AM To: gmx-us...@gromacs.org Subject: [gmx-users] (no subject) Dear Gromacs User, I simulated a coarse grained membrane protein system. This is my pressure control parameter. ; pressure control Pcoupl = berendsen ; Pcoupltype = semiisotropic ; tau-p= 5.0 5.0 ; compressibility = 4.5e-5 4.5e-5 ; ref-p= 1.0 1.0 1.0 1.0 ; refcoord_scaling = all ; Although I set Pcoupltype as semiisotropic, after running simulation a while, my box was changed from cubic (starting) to rectangular parallelepiped. the x,y direction were shortened while z direction was lengthened a lot. is there any option to control the box size through the simulation? Thank you so much. Hongtham -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Changing selections in Umbrella Sampling
Dear Users, I am doing umbrella sampling of pulling a protein away from a membrane. Initially I chose reaction coordinate to be the distance between com of the lower layer of the lipids and of the protein. After weeks of simulations, I have concluded a better selection of com - as the protein is positioned away from the center, only the membrane underneath should be used to measure the distance. Should I start from the very beginning, or I can actually stick to the last frame of the previous umbrella sampling and save times for equilibration? Looking forward to any experience sharing. Thanks in advance, Kevin City University of Hong Kong -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Atomtype OW not found
Hi, Does that script support such prehistoric versions of GROMACS? Mark On Wed, Jun 3, 2015 at 3:40 PM Rasha Alqus rasha.al...@manchester.ac.uk wrote: Dear Gromacs users, I am trying to run an md of carbohydrate systems in water, the pdb of carbohydrate produced in glycame builder, files were loaded in amber to produce topolgy file and coordinate using glycame force file. I have run glycam2gmx.pl script to convert files into gromacs ones. I would like to solavte the sytem using tip5p, but when i run the grompp i get an error program grompp_d, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OW not found For more information and tips for troubleshooting, please check the GROMACS I also tried to do that with other water model and it give me the same issue, can you please help me to solve that issue. Thank for the help Regards rasha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Atomtype OW not found
What does your topology (.top) file look like? And what's the exact command you are using for grompp? -- James “Wes” Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Rasha Alqus rasha.al...@manchester.ac.uk Sent: Wednesday, June 3, 2015 8:39 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Atomtype OW not found Dear Gromacs users, I am trying to run an md of carbohydrate systems in water, the pdb of carbohydrate produced in glycame builder, files were loaded in amber to produce topolgy file and coordinate using glycame force file. I have run glycam2gmx.pl script to convert files into gromacs ones. I would like to solavte the sytem using tip5p, but when i run the grompp i get an error program grompp_d, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OW not found For more information and tips for troubleshooting, please check the GROMACS I also tried to do that with other water model and it give me the same issue, can you please help me to solve that issue. Thank for the help Regards rasha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Looking for FF parameters for bivalent metals and oxoguanine
Hi Timofey, did you check http://ambermd.org/tutorials/basic/tutorial4b/ or https://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs cheers, Max On Jun 3, 2015, at 12:24 AM, Timofey Tyugashev tyugas...@niboch.nsc.rumailto:tyugas...@niboch.nsc.ru wrote: I'm investigating several protein-DNA systems with AMBER 99SB force field . Some of them involve 8-oxoG lesions and metal-dependent enzymes. Is there any reliable calculated parameters for them or any reliable and reasonably quick way to derive them? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] trjorder time-consuming
Dear GROMACS users, I am using the command gmx trjorder with a single frame of a trajectory, to order the water molecules according to the smallest distance to a molecule. The system is very small (4400 atoms), however gmx trjorder is taking more than 1 hour to finish!! Is it normal to be so time-consuming using only a single frame or maybe is there anything wrong with the execution? gmx trjorder -f frame.pdb -s topology.tpr -o frame_ordered.pdb -da 0 -na 3 Thanks a lot for your help in advance, Rebeca Dr. Rebeca García Santiago de Compostela University Spain -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] fix COM of a group
Hi Ming Tang, You didn't tell you were pulling... That's a totally different matter. I guess you want to use two pull groups and pull one with respect to the other. Cheers, Tsjerk On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Tsjerk, Thanks for your guidance. I add those two command lines you gave in .mdp, but got the following warnings. WARNING 1 [file dynamic.mdp]: Some atoms are not part of any center of mass motion removal group. This may lead to artifacts. In most cases one should use one group for the whole system. Number of degrees of freedom in T-Coupling group Protein is 8680.88 Number of degrees of freedom in T-Coupling group non-Protein is 202734.12 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.406 nm, buffer size 0.006 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm WARNING 2 [file dynamic.mdp]: You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts. Pull group natoms pbc atom distance at start reference at t=0 0 0 0 1 3 1919 -1.542 nm -1.542 nm Can I just ignore them? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 5:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Atomtype OW not found
Dear Gromacs users, I am trying to run an md of carbohydrate systems in water, the pdb of carbohydrate produced in glycame builder, files were loaded in amber to produce topolgy file and coordinate using glycame force file. I have run glycam2gmx.pl script to convert files into gromacs ones. I would like to solavte the sytem using tip5p, but when i run the grompp i get an error program grompp_d, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OW not found For more information and tips for troubleshooting, please check the GROMACS I also tried to do that with other water model and it give me the same issue, can you please help me to solve that issue. Thank for the help Regards rasha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem in energy minimization
Dear all, I am trying to set a coarse-grained MD for the membrane protein. After solvating, I met an error when running a short energy minimization ( 10 steps) before adding ions. Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps= 10 Step= 10, Dmax= 2.0e-05 nm, Epot= 2.76192e+20 Fmax= inf, atom= 8872 Reached the maximum number of steps before reaching Fmax 10 writing lowest energy coordinates. Steepest Descents did not converge to Fmax 10 in 11 steps. Potential Energy = 2.7619190e+20 Maximum force= inf on atom 8872 Norm of force =inf The reason is because of Maximum force is equal to infinity. Therefore I can not proceed further. Atom 8872 is water atom. Even when I delete this atom, the error occurs again with another water molecules, and goes on. Can someone help me figure out? and explain to me what happen? Is this because of overlapping problem? Thank you so much Jin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] temperature problem
Hi...Justin Thanks for explaining .. I just want to ask could
there be any other reasons too?? ...Because I have tried it with PME
too...and still I am not getting desired temperature
Thanks and Regards
Lovika
On Wed, Jun 3, 2015 at 5:29 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/3/15 3:46 AM, Lovika Moudgil wrote:
Hi...thanks for reply Peter and Mark I tried with temperature coupling
. But things are still same ...
Hi ... Mark would you like to explain this factor to me ??
Using a plain cutoff in the condensed phase is outdated methodology that
is very inaccurate. Cutoff artifacts lead to accumulation of heat in the
system. Use something sensible like PME.
-Justin
Thanks and Regards
Lovika
On Tue, Jun 2, 2015 at 2:23 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:
Hi,
Runaway heating is the only useful feature of cutoff electrostatics. Use
an
actual model physics.
Mark
On Tue, Jun 2, 2015 at 10:19 AM Peter Kroon p.c.kr...@rug.nl wrote:
On 02/06/15 09:43, Lovika Moudgil wrote:
Hi everyone
I am having some problem in my md run .In my system temperature of
system
is abruptly increasing .I have done nvt for 50 picoseconds ..nd then
using
it for further md simulation .I am not getting any error for this
temperature increase .But when I plot temperature graph ,
temperature
is not same as nvt and is very high in md .I am having gold slab and
amino
acid in my system . Mdp file for md run is below Is their any error
in
my mdp file ???what could be the reason for this ???Please suggest
; Run parameters
integrator= md; leap-frog integrator
nsteps= 3000; 2 * 5 = 100 ps
dt= 0.001; 2 fs
; Output control
; Output control
nstxout= 500; save coordinates every 1.0 ps
nstvout= 500; save velocities every 1.0 ps
nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps
nstxtcout = 500 ; [steps] freq to write
coordinates
to xtc trajectory
xtc_precision = 1000 ; [real] precision to write xtc
trajectory
xtc_grps= System; group(s) to write to xtc
trajectory
energygrps = System; group(s) to write to energy
file
; Bond parameters
constraint_algorithm= lincs; holonomic constraints
constraints= all-bonds; all bonds (even heavy
atom-H bonds) constrained
lincs_iter= 1; accuracy of LINCS
lincs_order= 4; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off
pme_order= 4; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= nose-hoover; modified Berendsen
thermostat
tc-grps= Protein AUS AUB AUI SOL NA CL; two coupling
groups -
more accurate
tau_t= 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ; time constant,
in ps
ref_t= 300 300 300 300 300 300 300; reference
temperature, one for each group, in K
You have too many temperature coupling groups. (What Not To Do on
http://www.gromacs.org/Documentation/Terminology/Thermostats)
I'd stick to one for proteins, and one for the rest.
; Pressure coupling is off
pcoupl= no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
; Velocity generation
gen_vel= yes; assign velocities from Maxwell
distribution
gen_temp= 300; temperature for Maxwell distribution
gen_seed= -1; generate a random seed
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps = AUS AUB AUI
freezedim= Y Y Y Y Y Y Y Y Y
comm_mode= None
Thanks and Reagrds
Lovika
Peter
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[gmx-users] error group protein not found
Hi every body I create a covalent bond and now I want to held MD by gromacs, after holding the following command : grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr I confornted to an error: Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. please let me know how can I solve this problem. I am looking forward to getting your answer thanks a lot -- *Marzieh DehghanPhD Candidate of BiochemistryInstitute of biochemistry and Biophysics (IBB)University of Tehran, Tehran- Iran.* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] trjorder time-consuming
On 6/3/15 8:52 AM, Rebeca García Fandiño wrote: Dear GROMACS users, I am using the command gmx trjorder with a single frame of a trajectory, to order the water molecules according to the smallest distance to a molecule. The system is very small (4400 atoms), however gmx trjorder is taking more than 1 hour to finish!! Is it normal to be so time-consuming using only a single frame or maybe is there anything wrong with the execution? No, that's not normal. Trajectories should finish in less time. gmx trjorder -f frame.pdb -s topology.tpr -o frame_ordered.pdb -da 0 -na 3 Does -da 1 make a difference? I wouldn't imagine COM vs. O position would substantially change the outcome, and you avoid having to calculate the COM for every molecule with -da 1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Invalid command line argument
On 6/3/15 1:35 PM, Poncho Arvayo Zatarain wrote: Hello: I'm doing Martínez Seara simulation and i want to run this command: echo 0|trjconv -f dppc128_1-nj-ct.xtc -s dppc128_1.tpr -o dppc128_1-nj -ct -nobox.xtc -box 100 100 100 but it appears: Invalid command line argument: -nobox.xtc Iḿ using GROMACS 5.0.2 and working in a cluster. What can i do? Read the help information and use valid options. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] URGENT query regarding pbc = no in grompp in membrane simulations
Why is this urgent? Have you tried the suggestions given by the program? Cheers, Tsjerk On Wed, Jun 3, 2015 at 12:08 PM, Antara mazumdar antara.mazum...@igib.in wrote: i want to simulate a system having membrane and proteins with pbc=no to allow surface effects. I use the following settings in my production mdp file : Run parameters integrator = md; leap-frog integrator nsteps = 1 ; 2 * 1 = 2 ms dt = 0.002 ; 2 fs ; Output control ;trr file nstxout = 50; save coordinates every 1ns nstvout = 50; save velocities every 1ns nstenergy = 1 ; save energies every 20ps nstlog = 1 ; update log file every 20ps ;xtc file nstxtcout = 1 ; xtc compressed trajectory output every 20 ps ; Bond parameters constraint_algorithm = LINCS; holonomic constraints constraints= none ;ns-type= simple nstlist = 0 rlist = 0 coulombtype = Cut-off rcoulomb= 0.0 rvdw= 0 Periodic boundary conditions pbc = no; 3-D PBC ; Velocity generation gen_vel = YES ; Velocity generation is on comm_mode = ANGULAR however i get LINCS warning and also the log file says this : Your simulation settings would have triggered the efficient all-vs-all kernels in GROMACS 4.5, but these have not been implemented in GROMACS 4.6. Also, we can't use the accelerated SIMD kernels here because of an unfixed bug. The reference C kernels are correct, though, so we are proceeding by disabling all CPU architecture-specific (e.g. SSE2/SSE4/AVX) routines. If performance is important, please use GROMACS 4.5.7 or try cutoff-scheme = Verlet. kindly suggest something .. -- Best *,* Antara -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] does gromos force field support implicit solvent?
Hi, Probably not - it wasn't parameterised for such usage, and any such re-deployment would require careful validation . Your background reading on your choice of model physics is your best guide to doing good physics. :-) Mark On Wed, 3 Jun 2015 07:55 Ming Tang m21.t...@qut.edu.au wrote: Dear gromacs experts, I tried to use gromos 54a7 force field to calculate persistence length of a helix in implicit solvent, but got GB parameters missing errors. When I tried to modify the implicit_genborn_params section, I found there is not gbsa.itp file in gromos54a7.ff does gromos force field support implicit solvent calculation? Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Invalid command line argument
Hello: I'm doing Martínez Seara simulation and i want to run this command: echo 0|trjconv -f dppc128_1-nj-ct.xtc -s dppc128_1.tpr -o dppc128_1-nj -ct -nobox.xtc -box 100 100 100 but it appears: Invalid command line argument: -nobox.xtc Iḿ using GROMACS 5.0.2 and working in a cluster. What can i do? Alfonso -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Questions about the topology file format
Hi there, I have two quick questions about the topology file format which I couldn’t find in the documentary. The semi-colon is giving me some headache. Is it always a comment which is written after? First: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_135 1 IPAC11-0.111600 12.01100 ; qtot -0.112 CT is qtot and CT used for anything and is it interpreted since it is after the ; Second: [ bonds ] ; ai aj funct r k 1 2 1 ;1.5350e-012.5363e+05 ; C1 - C2 CT - CT are the values for r and k here used since they are after the ; and what is C1-C2 and CT-CT used for and why another ;? Thank you very much for clarification. Max -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Questions about the topology file format
On 6/3/15 1:55 PM, Ebert Maximilian wrote: Hi there, I have two quick questions about the topology file format which I couldn’t find in the documentary. The semi-colon is giving me some headache. Is it always a comment which is written after? First: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_135 1 IPAC11-0.111600 12.01100 ; qtot -0.112 CT is qtot and CT used for anything and is it interpreted since it is after the ; Everything after ; is ignored. Second: [ bonds ] ; ai aj funct r k 1 2 1 ;1.5350e-012.5363e+05 ; C1 - C2 CT - CT are the values for r and k here used since they are after the ; and what is C1-C2 and CT-CT used for and why another ;? Not used for anything. Whatever software you used to produce the topology annotated it for whatever reason that the programmer decided was useful and in whatever manner he/she liked. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
