Re: [gmx-users] periodic boundary condition
Dear David, I tried to use x2top, but it ended up with the following error:0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field2: GROMOS96 43a2 force field (improved alkane dihedrals)3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)7: [DEPRECATED] Gromacs force field (see manual)8: [DEPRECATED] Gromacs force field with hydrogens for NMR9: Encad all-atom force field, using scaled-down vacuum charges10: Encad all-atom force field, using full solvent charges 0Looking whether force field file ffG43a1.rtp existsOpening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.rtpGenerating bonds from distances...Opening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.atpThere are 49 type to mass translationsatom 438---Program x2top, VERSION 3.3Source code file: futil.c, line: 537Fatal error:Library file ffG43a1.n2t not found in current dir nor in default directories.(You can set the directories to search with the GMXLIB path variable)Could you tell me what is wrong? Many thanks!!!CherryDavid van der Spoel [EMAIL PROTECTED] wrote: Cherry Y. Yates wrote: Dear gromacs developers and users, I am calculating a nanotube which has periodic boundary condition along one direction. I wonder how to make an itp file for this system. The difficulty lies in describing the bond between two end atoms, e.g., two atoms are bonded in an infinite length system, but are located on the bottom and top of a unit cell.use x2topand in your mdp file use pbc=full Thanks, Cherry Get your email and more, right on the new Yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University.Husargatan 3, Box 596, 75124 Uppsala, Swedenphone: 46 18 471 4205 fax: 46 18 511 755[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php Yahoo! Messenger with Voice. Make PC-to-Phone Calls to the US (and 30+ countries) for 2¢/min or less.___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] make_hole vs. genconf
Dear GMX Users, I'd like to build some lipids around a peptide. Can I do so using genconf? (I know genconf can be used to build a membrane. I'm asking if genconf can be used to build a membrane around a solute, like a transmembrane protein?) I'm also aware of the make_hole tool. My question here is: Does make_hole create a hole of specified dimensions and orientation, according to the solute coordinates? And can you specify exactly where in the membrane you want the whole? So basically what I'm asking is: If you want to make a starting structure (or several structures) with the solute (a peptide) in a specific part of the membrane, is it better to set the desired coordinates of the peptide first and then build a membrane around it? Or, is it wiser to start with an equilibrated membrane and use make_hole to create your hole first at the desired coordinates, then insert the peptide? Thanks, Arneh ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: velocities (gmx-users Digest, Vol 29, Issue 60)
Thanks for your answer. I hope I did not catch your points well. So, you mean I can use 'gen_vel = no' for the md runs (MD without position restraints, after the completion of PR run with position restarints) my procedure as follows.. EM --- PR(300ps @ 300K) MD (30ps @ 80K. no postion restraints)--- MD (30 ps @ 100K, no postion restraints ) --- MD (30 ps @ 200K, no postion restraints) relaxation MD(250ps @ 300K, no postion restraints) final MD (300K, no postion restraints) After Energy minimization, I apply position restarints and generate new velocities at 300K. I take the output of PR run as input to the next MD run which started at 80K ( no position restraints from now). And also from here onwards i dont generate any new velocities, but with the velocities which are written in the previous runs. Please let me know if iam correct or not. Thanks again Gajula Dear Gromacs Users, I am getting different results for simulations with gen_vel=yes and gen_vel= no. This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random number seed. What you want to do, is after equilibration, be sampling from the correct ensemble. I have generated velocities only for PR MD at 300K. after that I set ' gen_vel= no ' in mdp file. After the position restrained MD , I slowly increased the temparature from 80K , 100K , 200K and last 300K. (with 'gen_vel=no' for all MD) Is it correct? Because I read both 'yes' and 'no' as possibilites in some references. Iam bit confused which to use for exact simulations. Personally, I don't think the practice of velocity reassignment in incremental heating while using position restraints is demonstrably better than not using reassignment in incremental heating. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:velocities
Thanks for your answer. I hope I did not catch your points well. So, you mean I can use 'gen_vel = no' for the md runs (MD without position restraints, after the completion of PR run with position restarints) my procedure as follows.. EM --- PR(300ps @ 300K) MD (30ps @ 80K. no postion restraints)--- MD (30 ps @ 100K, no postion restraints ) --- MD (30 ps @ 200K, no postion restraints) relaxation MD(250ps @ 300K, no postion restraints) final MD (300K, no postion restraints) After Energy minimization, I apply position restarints and generate new velocities at 300K. I take the output of PR run as input to the next MD run which started at 80K ( no position restraints from now). And also from here onwards i dont generate any new velocities, but with the velocities which are written in the previous runs. Looking forward for your reply. Please let me know Thanks again Gajula Dear Gromacs Users, I am getting different results for simulations with gen_vel=yes and gen_vel= no. This is expected. No two simulations will be the same unless you run then on the same hardware with exactly the same inputs. gen_vel requires the use of a random number seed. What you want to do, is after equilibration, be sampling from the correct ensemble. I have generated velocities only for PR MD at 300K. after that I set ' gen_vel= no ' in mdp file. After the position restrained MD , I slowly increased the temparature from 80K , 100K , 200K and last 300K. (with 'gen_vel=no' for all MD) Is it correct? Because I read both 'yes' and 'no' as possibilites in some references. Iam bit confused which to use for exact simulations. Personally, I don't think the practice of velocity reassignment in incremental heating while using position restraints is demonstrably better than not using reassignment in incremental heating. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] single and double
[EMAIL PROTECTED] a écrit : My system here is an opls-aa protein in a POPE/DMPE membrane with tip4p waters. Prior to adding counterions, grompp yields a net charge of -1.73 and grompp_d yields -2.0. Once I have added counterions, both single and double precision don't give me a warning about a net charge on the system. Either system runs fine for many ns and they don't crash. 1. Is the net charge really as close to 0.0 in the single precision version as it is in the double, or just close enough that there is no warning issued? The net charge is really close to zero, the difference may rely on hardware roundoff, and on the topology limits (charge precision on each atom/group). This is why you see the difference between single and double precision. 2. If single is farther from 0.0, is this a problem? It depends :-) I assume you're using PME, in this case, the system will be scaled to 0 and for you run, that won't be a problem (since spreading a 1e-4 charges among 100 000 atoms won't interfere much with their net charge ...) and the roundoff errors due to the calculations themselves are bigger than this single vs double difference. 3. Why does single run faster anyway? I though intel processors treated them the exact same way in terms of the operations that needed to be carried out? It depends of the hardware you're talking about. On single precision systems, the run would run at the same speed on 32 bits architecture and on 64 bits architectures. On double precision systems, the same run will take twice the time on 32 bits than on 64bits (roughly). Globally, single precision == 32bits, double precision == 64bits. That means on single precision run on 32bits machines will be done in the same time that double precision on 64bits (roughly again). This is more or less true with gromacs since processors have more than two types of calculation units (thinkk of sse, sse2, 3Dnowext, ...) and gromacs is able to take most of them (if not all) into account via specialized routines, but that the goal. Thanks. Chris. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein unstable for parallel job while stable for serial one
Hi Akansha, Either you need to simulate both systems until you have full convergence before you can make conclusions regarding the (dis)similar behaviour or you have to test consistently, running replicate simulations both on one processor and on 16. That being said, it is very well possible that even between two simulations of the same system under completely identical conditions, except for the starting velocities and possibly the exact starting structure, you will get two completely different results. If you're protein can undergo a conformational change it's basically a matter of chance whether you observe it or not. Of course, I don't say it is not related to your simulation being distributed over multiple processors. It may be, but in order to exclude other effects you have to repeat simulations and/or work through the code very carefully. Which version of Gromacs did you use? Hope it helps, Tsjerk On 9/18/06, Akansha Saxena [EMAIL PROTECTED] wrote: Hello Has anybody seen a protein becoming unstable on parallel nodes while remaining stable on single node? I am running a NPT molecular dynamics simulation. The system contains a protein with 141 residues surrounded by water making the total to 32714 atoms. I ran this simulation at two places for 8ns. One as a serial job and the other as a parallel job on 16 nodes. The protein remains stable all through for the serial job but for parallel job the protein opens up after 3ns of simulation and is never stable after that. All other conditions are exactly the same. Any help would be highly appreciated. Akansha Akansha Saxena Graduate Student Department of Biomedical Engineering Washington University in St Louis __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: protein unstable for parallel job while stable for serial one
Akansha Saxena wrote: This is what I was doing. I was running exactly identical simulations on 1 processor and on 16 processors. By identical i mean - same starting structure, velocities taken from the same *.trr file. The only difference was the number of nodes for the production run. Well this sounds sensible, so long as you weren't doing an erroneous gen_vel = yes. But I give the same velocities and use exactly same starting structure for both simulations. Basically I use the same files for both cases. Only difference lying in the number of processors. I would think that with same intial conditions the calculations should be identical for both cases. Real-world floating point computations are not algebraic computations. You can divide a number n by x, and add the result to itself x times, and a test for equality against n will fail, for sufficiently pathological n and x. The order in which summation occurs when you have a mixture of large and small numbers can also affect the result through accumulated round-off errors. A parallel computation will effectively be doing this. The fact this happens is not actually a problem - the perturbation is not so large you are sampling a different ensemble. You just don't have algebraic reproducibility. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Co-variance Analysis
Hi Tsjerk, thank you for your help for the generation of the files. I found them. Please can you help me with some litle bit more information. 1) How many atoms did you used ?(it seems 1894 looking to the nr. of lines of the masses) 2) Are just normal masses or did you compute (mass_particle)^(1/2) 3) How many frames of the positions the particles are used? 4) How many eigenvalues in average are needed (the order of magnitude) for such a co-variance computation? Thank you in advance for your answer. Best regards Nicu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] make_hole vs. genconf
I'm also aware of the make_hole tool. My question here is: Does make_hole create a hole of specified dimensions and orientation, according to the solute coordinates? And can you specify exactly where in the membrane you want the whole? Make_hole doesn't actually make a hole. You need to make the premilinary hole yourself. Not true, I've made a hole using make_hole. Manually removing central lipids, and using make_hole to finess the rim of the hole is probably more computationally efficient, but make_hole is perfectly capable of doing what the name says (and less labor intensive). __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] umbrella sampling pull.pdo output
hi everyone
i'm trying to calculate the free energy of binding of
a guest and host in solution by umbrella sampling.
my pull groups consist of individual atoms on the host
and guest. i tried a force constant of 1/100*single
bond strength.
when the umbrella distance between the host and guest
atoms is set to {0.4,0.4,0.4} (i.e. .4 nm separation
in x,y, z), i notice that the pull.pdo file
eventually shows the separations in x,y,z becoming
very small - on the order of 0.02nm, which should
surely result in an energy explosion. however, a 100ps
simulation runs to completion with no complaints.
examining the distance between the 2 pulled atoms
using g_bond shows that they in fact remain around
0.7nm (=sqrt(3*.4^2)) apart, as expected. visual
inspection of the trajectory confirms that the pulled
atoms don't approach each other too closely.
is this perchance a bug or am i doing something wrong?
i start the simulation from a random configuration
selected from a long unconstrained nvt run using
grompp -f umbrella.mdp -o u4 -t nvt1.trr -time 100 -n
index.ndx (where index.ndx defines energy groups),
then run using
mdrun -s u4.trr -pi pull.ppa -pd u4 -pn pull.ndx.
my pull.ppa file looks like this:
verbose = yes
runtype = umbrella
reference_group = zn152
group1 = n204
reftype = com
k1 = 4393.2
pos1 = 0.4 0.4 0.4
and pull.ndx is:
[ zn152 ]
152
[ n204 ]
204
please let me know if more information is required to
understand the problem.
any suggestions would be greatly appreciated.
thanks
mo
ps - i also get an error running g_bond:
Fatal error:
No distribution(i0 = 999, i1 = 1)? ? ! ! ? !
with no histogram being output. i thought this may be
to do with the fact that the atoms aren't bonded, but
have yet to check on this.
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[gmx-users] VAL group
Title: VAL group Hello gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate group is made for the atoms in the valyl residue. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. Could something be wrong with the pdb2gmx program? Thank you in advance for any suggestions. Sincerely, Michael Owen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] make_hole vs. genconf
Great, thanks Chris! [EMAIL PROTECTED] wrote: I'd like to build some lipids around a peptide. Can I do so using genconf? (I know genconf can be used to build a membrane. I'm asking if genconf can be used to build a membrane around a solute, like a transmembrane protein?) around? No. I'm also aware of the make_hole tool. My question here is: Does make_hole create a hole of specified dimensions and orientation, according to the solute coordinates? And can you specify exactly where in the membrane you want the whole? Make_hole doesn't actually make a hole. You need to make the premilinary hole yourself. The general problem is that if you take out all lipids that contact the protein, then you will have a huge vaccuum aroung the protein. So first you take out all the lipids whose headgroup clashed (manually) then run make_hole to bend the tails out of the space that is to be occupied by the protein, then add the protien. You will need to install gromacs-3.1.4 to do this. So basically what I'm asking is: If you want to make a starting structure (or several structures) with the solute (a peptide) in a specific part of the membrane, is it better to set the desired coordinates of the peptide first and then build a membrane around it? Or, is it wiser to start with an equilibrated membrane and use make_hole to create your hole first at the desired coordinates, then insert the peptide? 1. Build your membrane (or find coords somewhere) 2. equilibrate it 3. Use make_hole or inflategro (I have never tried this one) http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis 4. re-equilibrate Reason not to do it all at once is because you want to limit your protein's exposure to vaccuum, although I suppose you could use position restraints to solve this issue (heavy atom on the protein and a z-only on the lipid phosphate). Chris ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: protein unstable for parallel job while stable for serial one
Hi Akansha (and Mark), The approach taken is indeed sensible, and in addition to that I fully support the comments made by Mark. It's actually part of what I meant, changing the number of processors gives you a difference between your simulations. However, it should not give you a consistent difference. That is, if you perform, say 100 simulations on 1 processor and 100 on 16, the results from one set should be similar to those obtained from the other. In casu, you should observe the conformational change approximately an equal number of times. The same would hold for full convergence of your system. In that case, the number of transitions (folding/unfolding, conformational change) should be approximately equal over a certain time and have the same rate, duration, etc. You'll only be able to get that for small systems. It is possible that the division over multiple processors introduces some artefacts, which was in fact found by Jelger Risselada some while ago (you can check the mailinglist archive). But I think this bug was fixed. You might be able to detect such a consistent effect in the results if you perform say five simulations on 1 processor and five on 16 processors, using different starting velocities. I hope this helps you a bit further. Best regards, Tsjerk On 9/19/06, Mark Abraham [EMAIL PROTECTED] wrote: Akansha Saxena wrote: This is what I was doing. I was running exactly identical simulations on 1 processor and on 16 processors. By identical i mean - same starting structure, velocities taken from the same *.trr file. The only difference was the number of nodes for the production run. Well this sounds sensible, so long as you weren't doing an erroneous gen_vel = yes. But I give the same velocities and use exactly same starting structure for both simulations. Basically I use the same files for both cases. Only difference lying in the number of processors. I would think that with same intial conditions the calculations should be identical for both cases. Real-world floating point computations are not algebraic computations. You can divide a number n by x, and add the result to itself x times, and a test for equality against n will fail, for sufficiently pathological n and x. The order in which summation occurs when you have a mixture of large and small numbers can also affect the result through accumulated round-off errors. A parallel computation will effectively be doing this. The fact this happens is not actually a problem - the perturbation is not so large you are sampling a different ensemble. You just don't have algebraic reproducibility. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] VAL group
Owen, Michael wrote: Hello gmx users, when I convert a pdb file of a peptide that contains a valyl residue into a .gro file a separate group is made for the atoms in the valyl residue. In what sense...? please include a relevant file excerpt, and the commands that created it. This has happened when OPLSAA/l and the GROMOS96 53a6 force fields were used. The molecule appears as one in the topology file, and the atomic description of the valyl residue in the pdb file matches that of the ffoplsa.rtp file. Have these forcefields really being modified for a radical, or are you really describing a valine residue? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: The molecule size (jiqing)
》Has this force field been demonstrated to be effective for this sort ofsimulation? If not, maybe you've begun to demonstrate that it isn't?Mark Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4, it was said thatgromos96 is not, however, recommended for use with long alkanes and lipids. So user has to validate force parameters. Now the problem is for a periodic boundary system, the density is ok but the Rg is too small. I feel the parameters for proper dihedrals need to be improved. Is it right? *Ji QingInstitute of Chemistry, Chinese Academy of SciencesTel: 0086-10-62562894 ，82618423* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: The molecule size (jiqing)
主月 ：） wrote: 》Has this force field been demonstrated to be effective for this sort of simulation? If not, maybe you've begun to demonstrate that it isn't? Mark Yes , you are quite right. In GMX manual 3.2, at the end of chapter 4, it was said that gromos96 is not, however, recommended for use with long alkanes and lipids. So user has to validate force parameters. Now the problem is for a periodic boundary system, the density is ok but the Rg is too small. I feel the parameters for proper dihedrals need to be improved. Is it right? It's likely that nobody knows. Find a force field that does work for such simulations, or read everything you can find on how to build force fields and do it from scratch. Modifying one sort of parameter is like taking a Beethoven symphony and substituting the second violin part with bass guitar line from Smoke on the Water. It might work, but you'd be mad to bet on it. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
