[gmx-users] Fw: ionic liquids
-- Original Message -- From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org Date: Sat, 30 Apr 2011 10:30:53 +0530 (GMT+05:30) Subject: ionic liquids Sir, I am trying to create an ionic-liquid system comprising of 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have generated the system using following command: genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb , well it created system of total 250 molecules 125 each but after equilibration the density is not matching with the reported.I tried simulated annealing procedure still no much difference. I wonder if there is any other way to generate an ionic liquid system or how the people do it tp reproduce the results , I urge for any quick suggestion. thanx, student. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Fw: ionic liquids
On 4/30/2011 5:20 PM, Prema Awati wrote: */-- Original Message --/* From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org Date: Sat, 30 Apr 2011 10:30:53 +0530 (GMT+05:30) Subject: ionic liquids Sir, I am trying to create an ionic-liquid system comprising of 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have generated the system using following command: genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb , well it created system of total 250 molecules 125 each but after equilibration the density is not matching with the reported.I tried simulated annealing procedure still no much difference. I wonder if there is any other way to generate an ionic liquid system or how the people do it tp reproduce the results , I urge for any quick suggestion. thanx, student. You can try to adapt the procedure here http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] sulfate ion
On 4/30/2011 3:54 PM, saly jackson wrote: Hi all I want to know about the ability of GROMACS to simulate sulfate in(SO4 (2-)), Do we can have the ion in our simulation using GROMACS? You asked this question on Wednesday, and got an answer. Googling sulfate gromacs finds that answer. If you learn to make better use of the free information resources at your finger tips, then you will probably find that people will be more inclined to help you later on when the answer to that problem is not a simple web search away. Our time is valuable to us, too :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Gromacs 4.5.4 MPI
On 4/30/2011 8:50 AM, Juliette N. wrote: Dear experts, I have successfully installed a normal gromacs 4.5.4 installation on one of my machines. I have read the Installation Instructions that As of GROMACS 4.5, threading is supported, so for e.g multi-core workstations, MPI is no longer required. Does this mean that there is no longer the need to do a second configuration with --enable-mpi? No, it means that --enable-mpi is not necessary for use of GROMACS in parallel on multi-core workstations. Thus, many situations will require it. Upon trying to configure using this command: ./configure --enable-mpi --program-suffix=_mpi There is an error as below: checking size of off_t... configure: error: in `/root/gromacs-4.5.4': configure: error: cannot compute sizeof (off_t) See `config.log' for more details. That error is found repeatedly in the archives. Your MPI compiler is not available and/or configured correctly. See the details in config.log. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] LINCS error- 4.5.4 installation?
On 4/30/2011 9:06 AM, Juliette N. wrote: Dear experts, I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few steps I get LINCS error: step 400, will finish Sat Apr 30 05:20:45 2011 Step 750, time 1.5 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 10.116560, max 72.359520 (between atoms 314 and 315) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 301302 61.00.1090 0.1841 0.1090 I tried to run using the same input files on 4.0.7 and simulation worked fine. I mean the LINCS is not because of flawed topology or instability issue. I am wondering this is happening because of MPI or installation ..Please help! Normally, a successful MPI installation would have produced an mdrun_mpi executable, not mdrun. 15 minutes before this email you didn't manage to configure successfully with --enable-mpi. So probably you are not running in parallel. Look at the number of .log files produced, and their first line. Regarding the LINCS error, your simulation was probably marginally stable, and got lucky with the integration in 4.0.7 and unlucky in 4.5. That's life - you should consider the management strategies here http://www.gromacs.org/Documentation/Terminology/Blowing_Up Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: Tcoupl default setting
On 4/30/2011 4:47 AM, Charlie Forde wrote: Thank you Mark for your response, In carrying out the test you recommended I realised that I had set the integrator to sd, in such a case the tcoupl parameter is ignored. This explains my well behave temperature in the absence of setting a tcoupl option. When I wrote the input file originally (months ago) I must have known what I was doing but then we live, we learn, we forget. Sure. Next time, if you post your .mdp file, someone will likely spot that for you... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4
×M5~˪yïxã]¹ß]7ãMuÓ Program mdrun, VERSION 4.0.7Source code file: checkpoint.c, line: 565Fatal error:Attempting to read a checkpoint file of version 12 with code of version 4-- 83_kargar-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-30 00.38, Mark Abraham wrote:
On 4/30/2011 5:05 AM, Sanku M wrote:
Hi David,
Actually, I had tried to use vsites to make this molecule rigid. I
read the manual section 4.7 as well. But, unfortunately, for a 5-site
tetrahedral geometry I was not able to figure out the right vsite type
I should use. So, I was wondering whether you can provide some input
on the details of how to use virtual sites for a tetrahedral molecule.
It would have been helpful.
David suggested using vsites as well as the multiple-constraints
approach, because the molecule needs to have its degrees of freedom
artificially increased to compensate for the artificial decrease.
A vsite could only work if there was some way to take four atoms for the
force calculation, project them into one (say COM), do the MD update
step on the COM, and project the update back out. I've no idea whether
that's sound or can be implemented, however.
It is quite involved. You need to keep the total mass constant and the
moments of inertia.
For instance for methane one could construct 4 mass-particles M on the
C-H bonds which are connected by 6 constraints. Then you can construct
the virtual positions of C and H based on those four masses. A real
methane has 5x3 degrees of freedom. The above construction has 4 masses
* 3 dof - 6 constraints = 6 degrees of freedom left. This would
therefore yield a correct rigid model.
Mark
Sanku
*From:* David van der Spoel sp...@xray.bmc.uu.se
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Fri, April 29, 2011 11:46:01 AM
*Subject:* Re: [gmx-users] rigid tetrahedral molecule
On 2011-04-29 17.55, gyorgy.han...@fc.up.pt
mailto:gyorgy.han...@fc.up.pt wrote:
Hi Sanku,
I've read about your problem just now, I don't know if it's already
solved but I had the same problem some weeks ago and I also had a lot of
troubles. But, finally I managed to solve it so maybe my experiences can
be helpful for you:
I think you should use SHAKE instead of LINCS. The manual says somewhere
that LINCS cannot be used when constraining triangles (i.e. angles) but
SHAKE works fine. On the other hand, if you use SHAKE you must switch
from domain decomposition to particle decomposition (if you run your
simulations parallel) just by using -pd when you type mdrun ('domain
decomposition = no' in the mdp file is not enough).
Then you must add as many constraints as degrees of freedom you have, so
9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work
with less than 9 but in my case I had to add 15 contraints. What I did
was the following:
First I constrained all P-F bonds then I constrained fictious F-F bonds
that I thought would make the molecule rigid. But it wasn't enough. Then
I added some more redundant F-F contraints (up to 15 in total) in a bit
arbitrary way until I found the 'magic combination'.
Now my simulations run perfectly.
Please note that if your rigid molecule has less than 6 degrees of
freedom your temperature will be incorrect!
You can achieve a solution with the right number of d.o.f. by using
vsites as well. How to do this is left as an exercise for the reader.
I hope this helps.
best,
Gyorgy
Citando Sanku M msank...@yahoo.com mailto:msank...@yahoo.com:
Thanks. The molecule was developed as a part of OPLS. The authors
used a
software called BOSS( developed in Bill Jorgensen's lab) . I guess this
softwares have way to perform rigid body motion. There are other
softwares like
DL-POLY which can perform rigid body MD. So, I guess, in those cases,
just
declaring a molecule 'rigid' might be good enough.
But, gromacs does not explicitly do rigid body MD. That's why I was
looking for
a trick .
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Sent: Wed, April 27, 2011 8:25:05 PM
Subject: Re: [gmx-users] rigid tetrahedral molecule
Sanku M wrote:
Hi,
I am interested in simulating a anionic molecule BF4(-) ( Boron
tetrafluoride). In the paper which developed the parameters for this
molecule,
it is mentioned that it has been used as 'rigid' molecule i.e the
molecule only
has non-bonding interaction but there was no intramolecular motion as
the
geometry was fixed.
I am trying to simulate this molecule in gromacs treating it as
rigid. But, I
was looking for best way to 'rigidify' this molecule.
I was wondering whether using LINCS to constrain all B-F and F-F
bonds will be
good enough . Or, Should I use virtual sites ? If I really need to
use virtual
site, will it be something like TIP5P water model ?
Can someone suggest the best wayout ?
Constraints should do the trick, but probably the best approach is to
simply
contact the authors who developed the model and ask how they did it.
Then you
know
Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4
On 4/30/2011 7:22 PM, Faezeh Kargar wrote: Dear gmx users, My code stops running because of electricity voltage oscillation. it happened for several times and each time I restarted running my code. but for this time with command mdrun -s topol.tpr -x traj.part0002.part0003.part0004.part0004.part0005.xtc -cpi state.cpt -e ener.part0002.part0003.part0004.part0004.part0005.edr -g md.part0002.part0003.part0004.part0004.part0005.log I used this command before without any error. but now I encountered error like this: Program mdrun, VERSION 4.0.7 Source code file: checkpoint.c, line: 565 Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 I looked at the file checkpoint.c. at first the version of checkpoint file is 4 but I do not know how and why it changes. The usual reason for this kind of error is that you're using an old version of GROMACS to access a file written by a new version. That's not a good idea. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Simulations in vacuo - energy increase
Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method. integrator = md tinit= 0 dt = 0.001 nsteps = 1000 nstxout = 2 nstvout = 2 nstfout = 0 nstlog = 10 nstenergy= 10 nstxtcout= 2 energygrps = Protein nstcomm = 5 nstlist = 0 ns-type = simple pbc = no rlist= 0 coulombtype = Cut-off rcoulomb = 0 epsilon_r= 2 vdw-type = Cut-off rvdw =0 Tcoupl = no tc-grps = Protein tau_t= 0.1 ref_t= 300 Pcoupl = no Pcoupltype = Isotropic tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Simulations in vacuo - energy increase
On 2011-04-30 14.17, Zoe Hall wrote: Gmx-users, I am trying to carry out a simulation of lysozyme in vacuo using the OPLS-AA forcefield. After energy minimisation, the protein is run for 10ps with position restraints and temperature coupling on. This is followed by the full production run of 10ns with temperature and pressure coupling turned off, H bonds are constrained using LINCS and a time step of 1fs. For vacuum conditions, the periodic boundary conditions are turned off, and no cut-offs are used. When I carry out the 10ns simulation the total energy gradually increases, as does the temperature from 300 to 500K. I presume this is because the temperature coupling is turned off, however that is what I have noted from the literature that others do for their vacuum simulations. Can anyone shed any light on this? Following is my method. integrator = md tinit = 0 dt = 0.001 nsteps = 1000 nstxout = 2 nstvout = 2 nstfout = 0 nstlog = 10 nstenergy = 10 nstxtcout = 2 energygrps = Protein nstcomm = 5 nstlist = 0 ns-type = simple pbc = no rlist = 0 coulombtype = Cut-off rcoulomb = 0 epsilon_r = 2 vdw-type = Cut-off rvdw =0 Tcoupl = no tc-grps = Protein tau_t = 0.1 ref_t = 300 Pcoupl = no Pcoupltype = Isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University _zoe.h...@chem.ox.ac.uk_ Are you sure h-bonds are being constrained, because otherwise the time step is too large? (maybe you need to write h-bonds). You may need to increase the constraint accuracy as well. We did all our vacuum calcs in double precision as well IIRC. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Alkanes, Alkens in Amber forcefield
Hi all I need .itp and .mdp files of some Alkanes such as Hepane, Decane and Heptene, Decene in Amber forcefield. Would you please help me? Best Regards Thanks alot Maria -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4
htmldiv On 4/30/2011 7:22 PM, Faezeh Kargar wrote: Dear gmx users, My code stops running because of electricity voltage oscillation. it happened for several times and each time I restarted running my code. but for this time with command mdrun -s topol.tpr -x traj.part0002.part0003.part0004.part0004.part0005.xtc -cpi state.cpt -e ener.part0002.part0003.part0004.part0004.part0005.edr -g md.part0002.part0003.part0004.part0004.part0005.log I used this command before without any error. but now I encountered error like this: Program mdrun, VERSION 4.0.7 Source code file: checkpoint.c, line: 565 Fatal error: Attempting to read a checkpoint file of version 12 with code of version 4 I looked at the file checkpoint.c. at first the version of checkpoint file is 4 but I do not know how and why it changes. The usual reason for this kind of error is that you're using an old version of GROMACS to access a file written by a new version. That's not a good idea. Mark Thank you for your reply. I just use version 4.0.7 of GROMACS and all of files are written by this version. as I said before, I could restart running of my codes with this command without any problem. Thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 83_kargar -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: ionic liquids
I am trying to create an ionic-liquid system comprising of 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have generated the system using following command: genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb , well it created system of total 250 molecules 125 each but after equilibration the density is not matching with the reported.I tried simulated annealing procedure still no much difference. I wonder if there is any other way to generate an ionic liquid system or how the people do it tp reproduce the results , I urge for any quick suggestion. You should report concrete values of density, topology and parameters, if you want help. -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Alkanes, Alkens in Amber forcefield
Maria Hamilton wrote: Hi all I need .itp and .mdp files of some Alkanes such as Hepane, Decane and Heptene, Decene in Amber forcefield. Would you please help me? Such species should be trivial to generate using antechamber (with GAFF, perhaps). There are various scripts to convert from Amber to Gromacs format. You may also be interested in acpype (http://code.google.com/p/acpype/). -Justin Best Regards Thanks alot Maria -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: ionic liquids
If you are sure about the force field (the one from Lopes et al.?) you are using, build a dilute system, and then run long enough simulations using NTP ensemble. possibly using simulation annealing. ? 2011-4-30 16:44, Vitaly Chaban ??: I am trying to create an ionic-liquid system comprising of 1-butyl-3-methyl-imidazolium(bmim) as cation and BF4-(bf4) as anion. I have generated the system using following command: genbox_d -cp bmim.gro -ci bf4.gro -nmol 125 -try 200 -o .pdb , well it created system of total 250 molecules 125 each but after equilibration the density is not matching with the reported.I tried simulated annealing procedure still no much difference. I wonder if there is any other way to generate an ionic liquid system or how the people do it tp reproduce the results , I urge for any quick suggestion. You should report concrete values of density, topology and parameters, if you want help. -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York 14627-0216 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] lyzosyme tutorial
Dear Justin I have started lyzosyme tutorial. when using the command pdb2gmx I get the following error. Please guide me to solve it thanks Regards D. Aghaie Program pdb2gmx, VERSION 4.0.99-dev-20100315 Source code file: /apps/gromacs/build/gromacs-4.5-beta3/src/kernel/pdb2top.c, line: 147 Fatal error: No force fields found (files with name 'forcefield.itp' in subdirectories ending on '.ff') For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] How to use Inflategro with different lipid types
Dear gromacs users, I am a new user of gromacs. I am currently trying to build a large bilayer with 3 different lipid species (11 DPPC : 7 POPC : 7 POPE) and no protein embedded in it. I have used single lipids from pre-equilibrated bilayers available at Mr. Tieleman's website. The distance of center of mass of neighboring lipids is 1 nm, so there are small areas with overlaps. I was hoping that I would be able to inflate my membrane and have the lipids totally free of overlaps using Inflategro. Subsequently, I was planning to use the shrinking steps to bring the membrane into physiological size. Is this strategy valid in the first place? If not, I kindly ask for an alternative. In case this method can be used, despite To identify the lipid species their actual residue name must be given which is mentioned in the methodology, the form INFLATEGRO bilayer.gro scaling_factor lipid_residue_name cutoff inflated_bilayer.gro gridsize areaperlipid.dat (protein) only allows the use of one lipid type. How is it possible to run perl with all lipid types at once? I have tried performing inflations using one lipid type at a time and they work. [It worths mentioning that the coordinates of the rest two (uninflated) lipid types slightly change without equilibration (I assume this has to do with Inflategro trying to force the molecules avoid overlaps)]. But I can't treat my membrane as a system that way. I have read the publication introducing the methodology, but it didn't help me solve my problem. I would be grateful if someone could help, also taking into account that I am inexperienced. Kindest regards, Yiannis -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
