RE: [gmx-users] x2top error in CNT simulation on Gromacs 3.3.3
Send a copy of your ffgmx.n2t, ffgmxbon.itp, and SWNT_6_6_144.pdb files please, if the following does not work. Also I think that the information updated in ffgmxbon.itp might be found in a different file with the 3.3.3 version (I think from looking at previous e-mails that it is ffencadvbon.itp). If any one could let me know I will make an addendum to my site for this new version. (I am about done using GROMACS due to the fact that I am graduating, so I will not be updating mine) ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA >-Original Message- >From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] >On Behalf Of Hero >Sent: Wednesday, April 23, 2008 5:44 PM >To: gmx-users@gromacs.org >Subject: [gmx-users] x2top error in CNT simulation on Gromacs 3.3.3 > >Dear All, > >I am trying to simulate water flow in CNT and just followed the website: >http://cs86.com/CNSE/SWNT.htm > >I did the following: > >1. ffgmx.n2t > must change this files name to ffencadv.n2t and add the following 2 >lines: >C C 1 C ; CNT Carbon with one bond >C C 2 C C ; CNT double bonded Carbon > >2. ffgmxbon.itp >add the following line to it: > ># >[ bondtypes ] >; i j func b0 kb >C C 1 0.14210 478900. ># >[ angletypes ] >; i j k func th0 cth >C C C 1 120.000 397.480 ># >[ dihedraltypes ] >; i l func q0 cq >C C 1 0.000 167.360 ># > >But when I ran: >x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp > >Error message appeared: >Can not find forcefield for atom C-1 with 2 bonds >. >Can not find forcefield for atom C-143 with 2 bonds >Can not find forcefield for atom C-144 with 2 bonds > >--- >Program x2top, VERSION 3.3.3 >Source code file: x2top.c, line: 206 > >Fatal error: >Could only find a forcefield type for 0 out of 144 atoms >--- >Could you please tell me what is the problem? This works on Gromacs 3.3.1 > >Thank you very much! > >Jue > > > >___ >_ >Be a better friend, newshound, and >know-it-all with Yahoo! Mobile. Try it now. >http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ >___ >gmx-users mailing listgmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! >Please don't post (un)subscribe requests to the list. Use the >www interface or send it to [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 search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Entropy correction in PMF
That sentence could definitely use some massaging. Try this: Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. This is because the work required to pull a ligand into a protein binding pocket depends on the concentration of that ligand in the unbound state. The entropic contribution, however, depends on the size of your simulation box if your sampling of the entire box is ergodic. Further, the large computational cost of converging the sampling of large separations between the protein and ligand make it undesirable to target true ergodicity for large separations. It is more efficient to calculate the work required to pull a ligand into a protein from an unbound state that has a defined concentration and then to separately calculate the work required to change that concentration to some standard state, e.g. 1 molar. If any other free energy users care to comment, perhaps we could come up with something based on what I have suggested (or something entirely different) that could go into the new manual. --original message -- I sent the attached message on last March 31 but I didn't get any answer... may be the right people was not available at that time and that is why I am trying again. I would thank a lot to have some more detail about this paragraph in the gromacs manual (version 3.3, chapter 6, page 111): Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. But when calculating a pmf between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed. Note that this term can be significant; when at 300K the distance is halved the contribution is 3.5 kJ mol-1.â why exactly for a substrate-protein complex shouldn't one correct the pmf? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] x2top error in CNT simulation on Gromacs 3.3.3
Dear All, I am trying to simulate water flow in CNT and just followed the website: http://cs86.com/CNSE/SWNT.htm I did the following: 1. ffgmx.n2t must change this files name to ffencadv.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon 2. ffgmxbon.itp add the following line to it: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 # [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 # But when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-1 with 2 bonds . Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms --- Could you please tell me what is the problem? This works on Gromacs 3.3.1 Thank you very much! Jue Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Installation problem on Mac OS X
Dear All, I am trying to install Gromacs-3.3.3 on a Power Mac G5 with the system version of Mac OS X 10.4.11 and kernel version of Darwin 8.11.0. After the successful installation of fftw-3.1.2 into a directory (using --prefix) of / programs/fftw312/, the installation of gromacs-3.3.3 failed. Here are the operations I did: ./configure --prefix=/programs/gromacs333 --exec-prefix=/programs/ gromacs333 make >& log Below is the output of the log file, indicating the problems. It failed at the point of "Set SIMD unit to use non-java rounding mode" in the ppc_altivec_util.h file. I am not sure whether this has something to do with the system configuration. Could anybody give me some suggestions on what's the problem and/or how to fix it? Many Thanks! Zuowei Making all in include Making all in . make[2]: Nothing to be done for `all-am'. Making all in types make[2]: Nothing to be done for `all'. Making all in src make all-recursive Making all in gmxlib Making all in nonbonded Making all in nb_kernel_ppc_altivec /bin/sh ../../../../libtool --tag=CC --mode=compile cc - DHAVE_CONFIG_H -I. -I../../../../src -I/usr/X11R6/include - I../../../../include -DGMXLIBDIR=\"/programs/gromacs333/share/top\" - I/programs/fftw312/include -O3 -fomit-frame-pointer -finline- functions -Wall -Wno-unused -mcpu=7450 -mtune=970 -MT nb_kernel010_ppc_altivec.lo -MD -MP -MF .deps/ nb_kernel010_ppc_altivec.Tpo -c -o nb_kernel010_ppc_altivec.lo nb_kernel010_ppc_altivec.c cc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/X11R6/include - I../../../../include -DGMXLIBDIR=\"/programs/gromacs333/share/top\" - I/programs/fftw312/include -O3 -fomit-frame-pointer -finline- functions -Wall -Wno-unused -mcpu=7450 -mtune=970 -MT nb_kernel010_ppc_altivec.lo -MD -MP -MF .deps/ nb_kernel010_ppc_altivec.Tpo -c nb_kernel010_ppc_altivec.c -o nb_kernel010_ppc_altivec.o In file included from nb_kernel010_ppc_altivec.c:27: ppc_altivec_util.h: In function 'set_non_java_mode': ppc_altivec_util.h:76: warning: implicit declaration of function 'vec_mfvscr' ppc_altivec_util.h:76: error: incompatible types in assignment ppc_altivec_util.h:77: warning: implicit declaration of function 'vec_sl' ppc_altivec_util.h:77: warning: implicit declaration of function 'vec_splat_u32' ppc_altivec_util.h:77: error: incompatible types in assignment ppc_altivec_util.h:78: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:79: warning: implicit declaration of function 'vec_or' ppc_altivec_util.h:79: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:80: warning: implicit declaration of function 'vec_mtvscr' ppc_altivec_util.h:80: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h: In function 'vec_zero': ppc_altivec_util.h:93: warning: implicit declaration of function 'vec_ctf' ppc_altivec_util.h:93: error: incompatible types in return ppc_altivec_util.h: In function 'vec_half': ppc_altivec_util.h:106: error: incompatible types in return ppc_altivec_util.h: In function 'vec_one': ppc_altivec_util.h:120: error: incompatible types in return ppc_altivec_util.h: In function 'vec_two': ppc_altivec_util.h:134: error: incompatible types in return ppc_altivec_util.h: In function 'vec_three': ppc_altivec_util.h:148: error: incompatible types in return ppc_altivec_util.h: In function 'vec_six': ppc_altivec_util.h:162: error: incompatible types in return ppc_altivec_util.h: In function 'vec_twelve': ppc_altivec_util.h:175: error: incompatible types in return ppc_altivec_util.h: In function 'load_xyz': ppc_altivec_util.h:195: warning: implicit declaration of function 'vec_lvsl' ppc_altivec_util.h:195: error: incompatible types in assignment ppc_altivec_util.h:196: warning: implicit declaration of function 'vec_lde' ppc_altivec_util.h:196: error: incompatible types in assignment ppc_altivec_util.h:197: error: incompatible types in assignment ppc_altivec_util.h:198: error: incompatible types in assignment ppc_altivec_util.h:199: warning: implicit declaration of function 'vec_perm' ppc_altivec_util.h:199: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:200: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:201: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:202: warning: implicit declaration of function 'vec_sld' ppc_altivec_util.h:202: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:203: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:204: warning: implicit declaration of function 'vec_mergeh' ppc_altivec_util.h:204: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h:206: error: AltiVec argument passed to unprototyped function ppc_altivec_util.h: In function 'load_vector_unaligned': ppc_altivec_util.h:225: error: inco
[gmx-users] Installation problem on Mac OS-X
Dear All, I am trying to install Gromacs-3.3.3 on a Power Mac G5 with the system version of Mac OS X 10.4.11 and kernel version of Darwin 8.11.0. After the successful installation of fftw-3.1.2 into a directory (using --prefix) of / programs/fftw312/, the installation of gromacs-3.3.3 failed. Here are the operations I did: ./configure --prefix=/programs/gromacs333 --exec-prefix=/programs/ gromacs333 make >& log Below is the output of the log file, indicating the problems. It failed at the point of "Set SIMD unit to use non-java rounding mode" in the ppc_altivec_util.h file. I am not sure whether this has something to do with the system configuration. Could anybody give me some suggestions on what's the problem and/or how to fix it? Many Thanks! Zuowei ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Entropy correction in PMF
I sent the attached message on last March 31 but I didn't get any answer... may be the right people was not available at that time and that is why I am trying again. I would thank a lot to have some more detail about this paragraph in the gromacs manual (version 3.3, chapter 6, page 111): “Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. But when calculating a pmf between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed. Note that this term can be significant; when at 300K the distance is halved the contribution is 3.5 kJ mol-1.” why exactly for a substrate-protein complex shouldn't one correct the pmf? Angel Piñeiro. On Sun, 2008-03-30 at 16:19 -0600, Ángel Piñeiro wrote: > Dear all, > > > > My question is related to the calculation of absolute binding Gibbs > energies more than to the use of Gromacs but it is motivated by a > paragraph of the Gromacs manual version 3.3 (and also on several > papers by Gilson, Karplus, and others), so I hope someone can help me. > > > > We have calculated the PMF curve along the distance between the center > of mass of a cyclodextrin (an oligosaccharide with a hydrophobic > cavity mimicking a pocket in a protein) and a surfactant of relatively > short aliphatic chain. Following the work of Gilson (several papers > published between 1997 and 2006 mainly in J Phys Chem B and Biophys. > J.), we hope to obtain a quantitative approach to the absolute binding > Gibbs energy from the integration of the Boltzmann factor for the pmf, > but our problem is whether or not we should perform before in this > curve the so-called entropic correction (also named by others volume > correction term). The abovementioned paragraph is in the page 111 (the > first page of chapter 6): > > > > “When a distance between two atoms or the centers of mass of two > groups is constrained or restrained, there will be a purely entropic > contribution to the pmf due to the rotation of the two groups. For a > system of two non-interacting masses the potential of mean force is: > > Vpmf (r) = (nc-1)kBT log(r) (6.1) > > where nc is the number of dimensions in which the constraint works > (i.e. nc = 3 for a normal constraint and nc = 1 when only the > z-direction is constrained).” > > > > I think that I understand the meaning and source of that term but the > paragraph follows: > > > > “Whether one needs to correct for this contribution depends on what > the pmf should represent. When one wants to pull a substrate into a > protein, this entropic term indeed contributes to the work to get the > substrate into the protein. But when calculating a pmf between two > solutes in a solvent, for the purpose of simulating without solvent, > the entropic contribution should be removed. Note that this term can > be significant; when at 300K the distance is halved the contribution > is 3.5 kJ mol-1.” > > > > I assume that our case is very similar to a substrate-protein complex > and then we should not correct the pmf, but I do not understand > exactly why not. > > > > > > Angel Piñeiro. > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [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 search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] couette flow
> Date: Wed, 23 Apr 2008 06:56:32 -0700 > From: [EMAIL PROTECTED] > Subject: RE: [gmx-users] couette flow > To: gmx-users@gromacs.org > > > > > --- On Wed, 4/23/08, Berk Hess <[EMAIL PROTECTED]> wrote: > > > From: Berk Hess <[EMAIL PROTECTED]> > > Subject: RE: [gmx-users] couette flow > > To: "Discussion list for GROMACS users" > > Date: Wednesday, April 23, 2008, 10:25 PM > > > Date: Wed, 23 Apr 2008 05:29:26 -0700 > > > From: [EMAIL PROTECTED] > > > Subject: RE: [gmx-users] couette flow > > > To: [EMAIL PROTECTED] > > > > > > > > > > > > > > > --- On Wed, 4/23/08, Berk Hess > > <[EMAIL PROTECTED]> wrote: > > > > > > > From: Berk Hess <[EMAIL PROTECTED]> > > > > Subject: RE: [gmx-users] couette flow > > > > To: [EMAIL PROTECTED] > > > > Date: Wednesday, April 23, 2008, 7:27 PM > > > > > Date: Wed, 23 Apr 2008 02:34:49 -0700 > > > > > From: [EMAIL PROTECTED] > > > > > To: gmx-users@gromacs.org > > > > > Subject: [gmx-users] couette flow > > > > > > > > > > Hi, > > > > > Has anyone here used gromacs to simulate > > couette flows > > > > in slit pores? I can see that it would be > > possible to use > > > > the pull code but I would like to be able to run > > in > > > > parallel. Any tips before I begin modifying > > source code > > > > would be greatly appreciated. > > > > > > > > > > Cheers, Matt > > > > > > > > I don't see what this has to do with the pull > > code. The > > > > pull code is made for forces between > > > > centers of mass of groups. > > > > > > > > There are already some external force options in > > the mdp > > > > file. > > > > > > > > But I don't see how you would set up an > > unbiased > > > > couette flow. > > > > In reality the flow is generated by a pressure > > difference. > > > > In a simulation you can apply an external force > > or impose a > > > > velocity profile. > > > > But both these options make presumptions about > > the > > > > force/flow profile. > > > > > > > > Berk. > > > > > > > > > > Couette flow is shear driven, all you need is to have > > one pore wall moving relative to the other. I figure this > > could be done using the pull code by assigning each wall to > > a different group and using the pull code to increase the > > lateral distance between them at a constant rate. But it > > seems that the pull code does not work in parallel. Is > > there another way to prescribe the motion of one of the > > walls? > > > Cheers, Matt > > > > Ah, sorry, I confused it with Poiseuille. > > > > The deform option does shear boundary conditions. > > > > But if you want to move real walls, there is currently no > > simple option that gives > > a group a constant velocity. The pull code should indeed do > > it. In the CVS version > > the pull code also works in parallel. > > > > BTW the reply address in your mail is your own address, > > instead of gmx-users, > > I don't you if you caused this, or if something is > > wrong on the server. > > > > Berk. > > > > > In that case I guess it would be easiest to switch to the CVS version. Thanks > for the tip. > Cheers, Matt I just realized that this will probably not work. I assume you have periodic walls. In that case one can not define a center of mass. The easiest way is probably editing the code and use the accelerate group option in the mdp file. It is not difficult to modify the update routine(s) in src/mdlib/update.c to apply a velocity instead of an acceleration. Another option would be to actually apply an acceleration to one of the walls and this will then result in a certain shear rate. Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatalerror: Couldnt write energies
Thanks David for reply. No,.edr which crahsed contain 216kb. sudheer babu wrote: >* Thanks Mark for your reply, My system is neither full nor didnt do *>* anything with .edr file, I did same simulation again, same problem I got *>* that stopped my simulation and showed "fatal error: could not write *>* energies" *>* Pls suggest me. *>* Thanks in advance * is your edr file exactly 2 Gb? >* *>* sudheer babu wrote: *>>*/ HI gmx-users, *>* />/ Iam simulating POPC lipids in water,I have done *>* />/ minimisation,equilibration and production, Till 2ns ran fine but when *>* />/ iam trying to run 2.5 ns run mid of the simulation at 18650 step it *>* *>* />/ crashed and showed error *>* / *>>*If the error is what's listed in your subject line, then you should *>>*investigate why it couldn't write energies - is your file system full, *>>*or did you do something silly with the energy file? *>* *>* *>* Mark *>* * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] urgent question
Thanks for everyone for the quick answers! Zsolt ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error:couldn't write energies
Thanks David for your reply . No, the crashed .edr has only 216kb. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Fatal error:couldnt write energies
sudheer babu wrote: Thanks Mark for your reply, My system is neither full nor didnt do anything with .edr file, I did same simulation again, same problem I got that stopped my simulation and showed "fatal error: could not write energies" Pls suggest me. Thanks in advance is your edr file exactly 2 Gb? sudheer babu wrote: / HI gmx-users, />/ Iam simulating POPC lipids in water,I have done />/ minimisation,equilibration and production, Till 2ns ran fine but when />/ iam trying to run 2.5 ns run mid of the simulation at 18650 step it />/ crashed and showed error / If the error is what's listed in your subject line, then you should investigate why it couldn't write energies - is your file system full, or did you do something silly with the energy file? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [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, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Fatal error:couldnt write energies
Thanks Mark for your reply, My system is neither full nor didnt do anything with .edr file, I did same simulation again, same problem I got that stopped my simulation and showed "fatal error: could not write energies" Pls suggest me. Thanks in advance sudheer babu wrote: >* HI gmx-users, *>* Iam simulating POPC lipids in water,I have done *>* minimisation,equilibration and production, Till 2ns ran fine but when *>* iam trying to run 2.5 ns run mid of the simulation at 18650 step it *>* crashed and showed error * >If the error is what's listed in your subject line, then you should >investigate why it couldn't write energies - is your file system full, >or did you do something silly with the energy file? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] couette flow
--- On Wed, 4/23/08, Berk Hess <[EMAIL PROTECTED]> wrote: > From: Berk Hess <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] couette flow > To: "Discussion list for GROMACS users" > Date: Wednesday, April 23, 2008, 10:25 PM > > Date: Wed, 23 Apr 2008 05:29:26 -0700 > > From: [EMAIL PROTECTED] > > Subject: RE: [gmx-users] couette flow > > To: [EMAIL PROTECTED] > > > > > > > > > > --- On Wed, 4/23/08, Berk Hess > <[EMAIL PROTECTED]> wrote: > > > > > From: Berk Hess <[EMAIL PROTECTED]> > > > Subject: RE: [gmx-users] couette flow > > > To: [EMAIL PROTECTED] > > > Date: Wednesday, April 23, 2008, 7:27 PM > > > > Date: Wed, 23 Apr 2008 02:34:49 -0700 > > > > From: [EMAIL PROTECTED] > > > > To: gmx-users@gromacs.org > > > > Subject: [gmx-users] couette flow > > > > > > > > Hi, > > > > Has anyone here used gromacs to simulate > couette flows > > > in slit pores? I can see that it would be > possible to use > > > the pull code but I would like to be able to run > in > > > parallel. Any tips before I begin modifying > source code > > > would be greatly appreciated. > > > > > > > > Cheers, Matt > > > > > > I don't see what this has to do with the pull > code. The > > > pull code is made for forces between > > > centers of mass of groups. > > > > > > There are already some external force options in > the mdp > > > file. > > > > > > But I don't see how you would set up an > unbiased > > > couette flow. > > > In reality the flow is generated by a pressure > difference. > > > In a simulation you can apply an external force > or impose a > > > velocity profile. > > > But both these options make presumptions about > the > > > force/flow profile. > > > > > > Berk. > > > > > > > Couette flow is shear driven, all you need is to have > one pore wall moving relative to the other. I figure this > could be done using the pull code by assigning each wall to > a different group and using the pull code to increase the > lateral distance between them at a constant rate. But it > seems that the pull code does not work in parallel. Is > there another way to prescribe the motion of one of the > walls? > > Cheers, Matt > > Ah, sorry, I confused it with Poiseuille. > > The deform option does shear boundary conditions. > > But if you want to move real walls, there is currently no > simple option that gives > a group a constant velocity. The pull code should indeed do > it. In the CVS version > the pull code also works in parallel. > > BTW the reply address in your mail is your own address, > instead of gmx-users, > I don't you if you caused this, or if something is > wrong on the server. > > Berk. > > In that case I guess it would be easiest to switch to the CVS version. Thanks for the tip. Cheers, Matt > > _ > Express yourself instantly with MSN Messenger! Download > today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. > Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] couette flow
> Date: Wed, 23 Apr 2008 05:29:26 -0700 > From: [EMAIL PROTECTED] > Subject: RE: [gmx-users] couette flow > To: [EMAIL PROTECTED] > > > > > --- On Wed, 4/23/08, Berk Hess <[EMAIL PROTECTED]> wrote: > > > From: Berk Hess <[EMAIL PROTECTED]> > > Subject: RE: [gmx-users] couette flow > > To: [EMAIL PROTECTED] > > Date: Wednesday, April 23, 2008, 7:27 PM > > > Date: Wed, 23 Apr 2008 02:34:49 -0700 > > > From: [EMAIL PROTECTED] > > > To: gmx-users@gromacs.org > > > Subject: [gmx-users] couette flow > > > > > > Hi, > > > Has anyone here used gromacs to simulate couette flows > > in slit pores? I can see that it would be possible to use > > the pull code but I would like to be able to run in > > parallel. Any tips before I begin modifying source code > > would be greatly appreciated. > > > > > > Cheers, Matt > > > > I don't see what this has to do with the pull code. The > > pull code is made for forces between > > centers of mass of groups. > > > > There are already some external force options in the mdp > > file. > > > > But I don't see how you would set up an unbiased > > couette flow. > > In reality the flow is generated by a pressure difference. > > In a simulation you can apply an external force or impose a > > velocity profile. > > But both these options make presumptions about the > > force/flow profile. > > > > Berk. > > > > Couette flow is shear driven, all you need is to have one pore wall moving > relative to the other. I figure this could be done using the pull code by > assigning each wall to a different group and using the pull code to increase > the lateral distance between them at a constant rate. But it seems that the > pull code does not work in parallel. Is there another way to prescribe the > motion of one of the walls? > Cheers, Matt Ah, sorry, I confused it with Poiseuille. The deform option does shear boundary conditions. But if you want to move real walls, there is currently no simple option that gives a group a constant velocity. The pull code should indeed do it. In the CVS version the pull code also works in parallel. BTW the reply address in your mail is your own address, instead of gmx-users, I don't you if you caused this, or if something is wrong on the server. Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] urgent question
Quoting Prettl Zsolt <[EMAIL PROTECTED]>: > Hello! > > I would like to use Cr3+ for my molecule modelling but I just could not find > a suitable one for Gromacs anywhere. If somebody has any suggestion, from > when can I download it, please write me ASAP, because it is very-very > important Step one - check the literature for evidence that someone has simulated this ion or developed parameters for it. If not, there may be a good reason. Read here: http://wiki.gromacs.org/index.php/Exotic_Species As a note on etiquette, it is often considered impolite to urgently request help because of the absolute, earth-shattering importance of your work. Our work is important too, and you're begging for someone's free time to attend to your needs :-) -Justin > > > > Thanks in advance, > > Zsolt > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa
On Wed, Apr 23, 2008 at 03:22:09PM +0400, Vasilii Artyukhov wrote: > > I'm afraid I have to use TIP5P; I _am_ looking at temperature dependent > information, and also, I need a good description of hydration of small > molecules I mentioned. These and other considerations make more or less > every other water model I know of (including TIPxP-Ew) at least twice less > attractive than TIP5P. So if TIP5P doesn't screw up the description of the > membrane as much as any other model would the water part, I think it will > do. if you could share your (future) experience with tip5p and membranes with us, that would be great. some time ago i decided to switch to all-atom simulations, and then had to make the choice between tip4p and tip5p. now for the life of me i don't remember *why*, but i do know that there were some strong arguments against tip5p. > 2008/4/22 Marc F. Lensink <[EMAIL PROTECTED]>: > > > > i'm very happily using berger/oplsaa/tip4p. mind that this means ua > > lipid tails and the rest aa, so unless you have a distinct lipid > > phase, it's probably not what you want. personally i'm not (yet) > > convinced it's a better combination than berger/gromos/spc, though. > > I'm sorry, I didn't quite understand the argument about 'having a distinct > phase'. Could you please elaborate? suppose there's a protein in your bilayer. if the lipids tails are berger, ie united-atom (ua), but the rest of the system, most importantly protein, is all-atom (aa), then you have an ua-aa contact region, which the force field is not parameterised for. i'd like to add that this is not necessarily a problem. current-day united-atom force fields already have ua-aa contacts when they use explicit hydrogens for polarised hydrogens (SOL, PHE, etc). > So, this leaves us with two votes for Berger/TIP4P and nothing at all about > CHARMM27. But it would be really nice to hear from someone who'd been using > the latter FF. (I realize that it might be smarter to ask such questions on > the CHARMM forum, but on the other hand, I'm still willing to do this in > GROMACS...) i hear very good stories about the charmm27 lipid tail parameters, but haven't used them myself. keep in mind that you will typically have to use surface tension terms to keep a correct area per lipid. not too long ago new dppc head group parameters were published, for use with charmm27, that do not require this surface tension term: Biophys J (2007) 92:4157. worth to check out, i'd say. cheers, marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] urgent question
Hi,
You probably didn't find it because it's not so popular for simulations.
My suggestion is to look very carefully in the literature. Transition
metals are difficult to models, especially when you need to take into
account both their interactions with water and with proteins - see e.g.:
@Article{Project:2008:J-Comput-Chem:18074346,
author = "Project, E and Nachliel, E and Gutman, M",
title = {Parameterization of Ca+2-protein interactions for molecular dynamics
simulations},
abstract = {Molecular dynamics simulations of Ca+2 ions near protein were
performed with three force fields: GROMOS96, OPLS-AA, and CHARMM22. The
simulations reveal major, force-field dependent, inconsistencies in the
interaction between the Ca+2 ions with the protein. The variations are
attributed to the nonbonded parameterizations of the Ca+2-carboxylates
interactions. The simulations results were compared to experimental data, using
the Ca+2-HCOO- equilibrium as a model. The OPLS-AA force field grossly
overestimates the binding affinity of the Ca+2 ions to the carboxylate whereas
the GROMOS96 and CHARMM22 force fields underestimate the stability of the
complex. Optimization of the Lennard-Jones parameters for the Ca+2-carboxylate
interactions were carried out, yielding new parameters which reproduce
experimental data.},
journal = "J Comput Chem",
year = "2008",
volume = "29",
number = "7",
pages = "1163-1169",
month = "May",
pmid = "18074346",
url = "http://www.hubmed.org/display.cgi?uids=18074346";,
doi = "10.1002/jcc.20876"
}
Ran.
Prettl Zsolt wrote:
> Hello!
>
> I would like to use Cr3+ for my molecule modelling but I just could
> not find a suitable one for Gromacs anywhere. If somebody has any
> suggestion, from when can I download it, please write me ASAP, because
> it is very-very important
>
>
>
> Thanks in advance,
>
> Zsolt
>
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
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___
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[gmx-users] urgent question
Hello! I would like to use Cr3+ for my molecule modelling but I just could not find a suitable one for Gromacs anywhere. If somebody has any suggestion, from when can I download it, please write me ASAP, because it is very-very important Thanks in advance, Zsolt ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa
Thanks Chris and Mark! 2008/4/21 Chris Neale <[EMAIL PROTECTED]>: > I use tip4p/opls/berger combination and it works well for me. I have never > used tip5p. I suggest that you build your membrane and run one control > simulation (sounds like you would lean toward using spc for this) and then > one simulation with tip5p. Check order parameters and > area per lipid while using anisotropic pressure coupling. > Surely I'll try to see for myself how bad different water models perform :) Still, I was hoping that I could get some info beforehand (like if someone told me that TIP5P absolutely screws up the results for Berger; such kind of advice can really save one time). Also, are you sure that you want to use tip5p? > > Chris. I'm afraid I have to use TIP5P; I _am_ looking at temperature dependent information, and also, I need a good description of hydration of small molecules I mentioned. These and other considerations make more or less every other water model I know of (including TIPxP-Ew) at least twice less attractive than TIP5P. So if TIP5P doesn't screw up the description of the membrane as much as any other model would the water part, I think it will do. 2008/4/22 Marc F. Lensink <[EMAIL PROTECTED]>: > > i'm very happily using berger/oplsaa/tip4p. mind that this means ua > lipid tails and the rest aa, so unless you have a distinct lipid > phase, it's probably not what you want. personally i'm not (yet) > convinced it's a better combination than berger/gromos/spc, though. > > cheers, > marc > I'm sorry, I didn't quite understand the argument about 'having a distinct phase'. Could you please elaborate? So, this leaves us with two votes for Berger/TIP4P and nothing at all about CHARMM27. But it would be really nice to hear from someone who'd been using the latter FF. (I realize that it might be smarter to ask such questions on the CHARMM forum, but on the other hand, I'm still willing to do this in GROMACS...) Thanks again, Vasilii ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
FW: [gmx-users] couette flow
From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: RE: [gmx-users] couette flow Date: Wed, 23 Apr 2008 11:57:17 +0200 > Date: Wed, 23 Apr 2008 02:34:49 -0700 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] couette flow > > Hi, > Has anyone here used gromacs to simulate couette flows in slit pores? I can > see that it would be possible to use the pull code but I would like to be > able to run in parallel. Any tips before I begin modifying source code would > be greatly appreciated. > > Cheers, Matt I don't see what this has to do with the pull code. The pull code is made for forces between centers of mass of groups. There are already some external force options in the mdp file. But I don't see how you would set up an unbiased couette flow. In reality the flow is generated by a pressure difference. In a simulation you can apply an external force or impose a velocity profile. But both these options make presumptions about the force/flow profile. Berk. Express yourself instantly with MSN Messenger! MSN Messenger _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] couette flow
Hi, Has anyone here used gromacs to simulate couette flows in slit pores? I can see that it would be possible to use the pull code but I would like to be able to run in parallel. Any tips before I begin modifying source code would be greatly appreciated. Cheers, Matt Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp error, invalid line in .gro file [SOLVED]
Your formatting is incorrect. The .gro format is a very old GROMOS fixed format (not free format). See the manual for the details: http://www.gromacs.org/documentation/reference/online/gro.html Thanks a lot. Now everything works perfectly! /Andreas ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] trjconv error
Hi, Thanks for the mail. Well, I am using a old version specifically, even though newer versions are available. It is quite confusing since the same file is being able to be read by other tools like gmxcheck. And it is while running by gmxcheck that I get the Magic number error Raghu --- On Wed, 23/4/08, Mark Abraham <[EMAIL PROTECTED]> wrote: > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] trjconv error > To: "Gromacs Users" > Date: Wednesday, 23 April, 2008, 11:44 AM > Ragothaman Yennamalli wrote: > > Hi, > > Sorry for not replying immediately. > > > > Gromacs ver 3.2.1 > > OS is Red hat enterprise 4 > > Initially I had tried reading the file from an > external hard disk and now I copied it to another system > and tried again. Still the same error. > > The reason why I was truncating was due to a magic > number error I got while reading the trajectory. > > "Fatal error: Magic Number Error in XTC file > (read 0, should be 1995)" > > So, I was truncating it at an earlier time from where > I didnt see any errors. > > Dunno. 3.2.1 is a very old version - you should be planning > your upgrade > to version 4 as soon as it's out, unless you need > compatibility for some > reason. > > Otherwise the only reason I can think that gmxdump might > succeed where > trjconv doesn't is that it isn't actually an XTC > file, but some other > format with an .xtc extension. > > Try to replicate your problem with a small simulation. If > you can, then > you probably have a real issue, but this is very unlikely. > If you can't > replicate it, then it seems you've probably mangled > something and we > can't help you. > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. > Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] free energy calculation
So, obviously, no one knows how to do that by g_lie. Most people here compute free energies by TI. Do some background reading and find out yourself how it works. Posting mails twice or more won't help you regards Maik Goette, Dipl. Biol. Max Planck Institute for Biophysical Chemistry Theoretical & computational biophysics department Am Fassberg 11 37077 Goettingen Germany Tel. : ++49 551 201 2310 Fax : ++49 551 201 2302 Email : mgoette[at]mpi-bpc.mpg.de mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ shuai lu wrote: Hi everyone, I want to calculate free energy between protein and ligand by "g_lie" command. So the average Coulomb interaction and average Lennard-Jones interaction of ligand-solvent are need. But I do not know if average Coulomb interaction is the result of "Coul-SR" plus "Coul-14", which are calculated by "g_energy" command, and also if Lennard-Jones interaction is the result of "LJ-SR" plus "LJ-LR" plus "LJ-14". Hence I hope anyone who know about them may help me kindly. Thank you! -- Lu Shuai ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [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 search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
