[gmx-users] free energy calculations using MBAR and gromacs
Hi, I am trying to calculate free energy of a system that involves disappearance of LJ particle at lambda=1 in explicit solvent. I ran the simulation at 20 different lambda points ranging from 0 to 1, using soft core potential. In order to use MBAR method (python implementation from Michael shirts ), I have to rerun the simulations, in order to get potential energies for each configuration at every lambda point. Now, here i get into trouble. If i evaluate the trajectories generated at lambda = 1 (particle completely decoupled) using the potential function at lambda = 0, i get very large energy values, which quite likely are responsible for MBAR's failure to converge . The program works well if i calculate free energy to/from an intermediate. ie lambda 0 -> 0.5 and 0.5->1.0 As the potential energies for the configurations generated at lambda=1, evaluated using potential energy function at lambda =0, is expected to be infinite (due to Van der Waals overlaps between solvent and LJ particle), Is it even possible to apply MBAR method to such cases, without splitting the analysis to an intermediate lambda value? Did anyone ran into similar problems, or am i missing something? With Regards, Gurpreet -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] broken molecules in ouput of MDRUN
Dear Users, I am simulating a binary mixture of cyclohexane-water using gromacs 4.0.4. Every thing works fine except that the output trajactory (.xtc file) contains broken molecules. Interestingly enough, as the last frame of simulation is also dumped as gro file, has all the molecules as a whole, where as same frame in xtc file(the last frame) is broken. I searched the mailing list and found out that few other users have also complained about it. http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Does this mean that I have to run trjconv after every simulation to get the molecules as whole or it is a bug. With Regards, Gurpreet Singh ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sas and PBC
Gurpreet Singh wrote: > Dear Gromacs Users, > > I am using g_sas program of gromacs to calculate SASA, ?using -pbc flag. > It seems to me that the program does not take into account the periodic > boundary conditions. > Even thought this problem is mentioned in the mailing list, it still not > clear whether the program can or cannot take into account the > periodicity. > i am using gromacs3.3.2 . Could anyone please clarify this. > http://bugzilla.gromacs.org/show_bug.cgi?id=180 I downloaded the gromacs 3.3.3 and carried out some test calculations. The PBC is still not working, at least with test i have performed. I generated a trajcetory file containing two atoms in a cubic box of 4nm having same x and y coordinates and varied the z coordinates of one of the atoms. one atom is fixed at z coordinate of 3.9. The result of sasa vs coordinates is as follows: Step noz coordinate total_sasa 1 2.0500074506 14.1497 2 2.1000149012 14.1497 3 2.1500223517 14.1497 4 2.2000298023 14.1497 5 2.2500372529 14.1497 6 2.3000447035 14.1497 7 2.3500521541 14.1497 8 2.4000596046 14.1497 9 2.4500670552 14.1497 10 2.5000745058 14.1497 11 2.5500819564 14.1497 12 2.6000894070 14.1497 13 2.6500968575 14.1497 14 2.7001043081 14.1497 15 2.7501117587 14.1497 16 2.8001192093 14.1497 17 2.8501266599 14.1497 18 2.9001341105 14.1497 19 2.9501415610 14.1497 20 3.0001490116 14.1497 21 3.0501564622 14.1497 22 3.1001639128 14.1497 23 3.1501713634 14.1497 24 3.2001788139 14.1497 25 3.2501862645 14.1497 26 3.3001937151 14.1497 27 3.3502011657 13.7971 28 3.4002086163 13.1359 29 3.4502160668 12.5849 30 3.5002235174 11.9237 31 3.5502309680 11.3727 32 3.6002384186 10.7115 33 3.6502458692 10.1605 34 3.7002533197 9.49926 35 3.7502607703 8.94826 36 3.8002682209 8.39726 37 3.8502756715 7.51566 38 3.9002831221 14.1497 39 3.9502905726 7.51566 402.980232238769531E-008 14.1497 415.03054738045E-002 14.1497 420.10031292439 14.1497 430.15032037497 14.1497 440.20032782555 14.1497 450.25033527613 14.1497 460.30034272671 14.1497 470.35035017729 14.1497 480.40035762787 14.1497 490.45036507845 14.1497 500.50037252903 14.1497 510.55037997961 14.1497 520.60038743019 14.1497 530.65039488077 14.1497 540.70040233135 14.1497 550.75040978193 14.1497 I used the following command to calculate the sasa g_sas_d -f test.xtc -s topol.tpr -pbc -ndots 500 I can attached the tpr and xtc file if needed With Regards, Gurpreet singh ___ 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] g_sas and PBC
Dear Gromacs Users, I am using g_sas program of gromacs to calculate SASA, using -pbc flag. It seems to me that the program does not take into account the periodic boundary conditions. Even thought this problem is mentioned in the mailing list, it still not clear whether the program can or cannot take into account the periodicity. i am using gromacs3.3.2 . Could anyone please clarify this. With Regards, Gurpreet Singh ___ 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] problem in recognising the atom type
Thanks Mark You said OS is not defined in 43a1 force field, so is their any way out for that or i have to use a different force field. Actually i tried using the OPLS force field but in that case i was getting the similar error but this time at the CH3 atom. ie 'CH3 atom not found' Which is the better force filed for these types of simulation involving these organic compunds ? Thanks & Regards Gurpreet On 8/23/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > gurpreet singh wrote: > > Hello Users > > > > I am using gromacs 3.3 with the force field 43a1. > > > > I have an organic compund in my simulation so i used the Dundee Prodrg2 > > server for getting the .itp file. Then i added the corresponding .itp > > file in the top file . > > While running the grompp i am getting the following error > > Fatal error: > > Atomtype 'OS' not found! > > OS is one of the atom type in the .itp file generated above. i have > > checked in the manual this is a well defined atom type so what else > > could be the reason for this problem. > > OS is not defined in 43a1. > > 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 > ___ 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] problem in recognising the atom type
Hello Users I am using gromacs 3.3 with the force field 43a1. I have an organic compund in my simulation so i used the Dundee Prodrg2 server for getting the .itp file. Then i added the corresponding .itp file in the top file . While running the grompp i am getting the following error Fatal error: Atomtype 'OS' not found! OS is one of the atom type in the .itp file generated above. i have checked in the manual this is a well defined atom type so what else could be the reason for this problem. Waiting for your early reply Thanks & Regards Gurpreet ___ 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] problem regarding the aspartic acid representation
Helllo users It seams that gromacs can only take Aspartate not aspartic acid. Is it true? If no than what is the way to do that I am using the G43a1 force field during pdb2gmx Thanks & Regards Gurpreet ___ 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] problems with parallel mdrun
Dear gmx users, I am using a current CVS version of Gromacs and using the newly introduced options for simulations with walls. I am facing the following two problems. I get the following errors while using paralled version of mdrun compiled with openmpi. mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1 * Program mdrun_d_mpi, VERSION 3.3.99_development_20070720 Source code file: gmx_parallel_3dfft.c, line: 90 Fatal error: nx (50) and ny (50) must be divisible by the number of nodes (4). *** I am using a cubic box of 5nm and grid spacing is 0.1. The simulations runs fine if i use 5 nodes I am using a machines with 2 dual xeon processors so -np 4 is more appropriate for my sytems. Is there any way to use -np 4 without changing the gridspacing or box size? second question is regarding wall_denstiy option. As i understood from the manual the wall density is a number density in units of number/nm2 in case of 10-4 potential and is number/nm3 in case of 9-3 potential. please correct me if i am wrong. Thank you in advance With Regards, Gurpreet ___ 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] problem regarding total time elapsed
Hello users I am using gromacs 3.3 with 43a1 force field. My question is that if i run a simulation say for 50ns , Then if i carried out another md after this one than its time should start from ahead of 50 and not again from the beginning. but in my case everytime the time starts from the beginning. I know its a very basic question which i should not ask from the intelligentsia but this is irritating me from quiet a long time. so please tell me if this is a usual behaviour or some mistake is there in the input file input file : title= third at contant pressure equilibration integrator = md dt = 0.002 nsteps = 25000 nstxout = 500 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME vdwtype = cut-off Tcoupl = berendsen pcoupl = berendsen tau_t= 0.1 0.1 0.1 tc_grps = protein SOLCL- ref_t= 300 300 300 ref_p= 1 1 1 tau_p= 1 1 1 compressibility = 4.5e-5 4.5e-5 4.5e-5 pcoupltype = isotropic define = -DPOSRES comm_mode= angular constraints = hbonds constraint_algorithm = shake gen_vel = yes gen_temp = 300 After every run i am using the output gro file as an input for the next run Thanks & Regards ___ 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] doubt in minimization
Hello users I am carrying a protein simulation using gromacs 3.3 and g43a1 force field. My doubt is that when i carried out minimization i found that that in the log file there were no energy terms corresponding to some steps, althouigh minimization went fine without any problem . What could be the reason for this ? can i beleive the data obtained from that minimization ? Thanks With regards Gurpreet ___ 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] question regarding restraints
Thanks David for your quick reply
you were write actually , there is no energy term corresponding to the
postional restrain in the log file,
but i am using the proper posre.itp file created by genpr command (restrain
for whole protein) ,
genpr -f 4min_ion_water.pdb -o posre.itp -fc 50
then i have included define also in my .mdp file corresponding to this
restrain file
i used grompp in the following way
grompp -f 6eq_w.mdp -c 5min_w.gro -p aquapo_grom.top -r posre.itp -o
6eq_w.tpr
then what else i should check to rectify this problem ?
{ Actually my protein is a dimer, earlier two .itp files were crested by
pdb2gmx in the beginning but to reduce the restrain and to include all the
hydrogens added this time in the restrain file i made another .itp file.}
With regards
Gurpreet
On 7/21/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
gurpreet singh wrote:
> Hello users
>
> I am using the gromacs 3.3 with 43a1 force field.
> I am using a restraint force of 50 intially during the beginning of
> protein simulation in water, even after such a high value of restraint
> force i can see some major deviations in my structure during the
> simulation.
>
> My doubt is that since i am applying enough restrain force on the
> protein it should not deviate at all from its native conformation.
> I want to know is this the usual behavior in gromacs or i am making some
> mistake in applying restrain.
>
> I am using a posre.itp file using define = -dposre in the .mdp file for
> applying the restraining force.
>
are you sure the restraints are applied? check whether you have an
energy term corresponding to it. typical force constants people use are
1000 kJ/mol/nm^2
>
> With regards
> Gurpreet
>
>
>
>
>
> ___
> 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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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se
___
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[gmx-users] question regarding restraints
Hello users I am using the gromacs 3.3 with 43a1 force field. I am using a restraint force of 50 intially during the beginning of protein simulation in water, even after such a high value of restraint force i can see some major deviations in my structure during the simulation. My doubt is that since i am applying enough restrain force on the protein it should not deviate at all from its native conformation. I want to know is this the usual behavior in gromacs or i am making some mistake in applying restrain. I am using a posre.itp file using define = -dposre in the .mdp file for applying the restraining force. With regards Gurpreet ___ 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] problem with genion
Thanks Tsjerk I referred the mail about the broken molecules but there the problem is i think somewhat different. in that case broken molecules are coming becasue of the PBC . since PBC is being used that is why some part of the molecule is coming from the other side of box and its looking as if protein is broken but in my case i think the situation is different, first of all i have not still started using the PBC in the simulation and my full molecule (broken molecule) is right in the center of the box. moreover i am getting this problem before starting any simulation. till i did some simulation in vaccum before adding ions , it went fine there and then while shifting to the water simulation i added ions and right after adding the ions my molecule is getting broken. Thanks With Regards Gurpreet 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Gurpreet, I didn't ask whether you used PBC, I suggested it was due to PBC. Check the archives for "broken molecules" and such. Tsjerk On 7/16/07, gurpreet singh <[EMAIL PROTECTED]> wrote: > Thanks Tsjerk for you reply > i did not get your point . i think you are asking me whether i used PBC or > not , so i want to tell you that the .tpr file which i used for genion > command was created without using PBC. > > but will it make any difference ? > > Thanks > With Regards > Gurpreet > > On 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED] > wrote: > > > > Gurpreet, > > > > > my system was going fine at that time but when i used the genion > command to > > > add ions , i found that my protein was broken into parts. > > > what could be the reason for this ? > > > > PBC? > > > > > While running the genion it usually asked for the group into which we > want > > > to add the ions so i have checked with both the SOL group and OTH group > > > seperatly , in both the cases ions were replacing the solvent molecules. > Is > > > their any way by which we can add ions without replacing any solvent > > > molecules ? > > > > No, there's no space to put them. > > Well, you could try to squeeze them in here or there manually, and > > perform energy minimization... > > > > Cheers, > > > > Tsjerk > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > Junior UD (post-doc) > > Biomolecular NMR, Bijvoet Center > > Utrecht University > > Padualaan 8 > > 3584 CH Utrecht > > The Netherlands > > P: +31-30-2539931 > > F: +31-30-2537623 > > ___ > > gmx-users mailing list gmx-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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] problem with genion
Thanks Tsjerk for you reply i did not get your point . i think you are asking me whether i used PBC or not , so i want to tell you that the .tpr file which i used for genion command was created without using PBC. but will it make any difference ? Thanks With Regards Gurpreet On 7/16/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Gurpreet, > my system was going fine at that time but when i used the genion command to > add ions , i found that my protein was broken into parts. > what could be the reason for this ? PBC? > While running the genion it usually asked for the group into which we want > to add the ions so i have checked with both the SOL group and OTH group > seperatly , in both the cases ions were replacing the solvent molecules. Is > their any way by which we can add ions without replacing any solvent > molecules ? No, there's no space to put them. Well, you could try to squeeze them in here or there manually, and perform energy minimization... Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] problem with genion
Hello users, I am carrying a protein simulation using g43a1 force field in gromacs 3.3 i carried out some intial simulation without water in the absence of the neutralizing ions my system was going fine at that time but when i used the genion command to add ions , i found that my protein was broken into parts. i am using genion -s 4min.tpr -o 4min_ion.pdb -nname CL- -nn 6 -g 4min_ion2.log i have checked upto 4min.tpr , structure is fine but only after adding ions i am getting this breakage i.e in the file 4min_ion.pdb what could be the reason for this ? While running the genion it usually asked for the group into which we want to add the ions so i have checked with both the SOL group and OTH group seperatly , in both the cases ions were replacing the solvent molecules. Is their any way by which we can add ions without replacing any solvent molecules ? Thanks With Regards Gurpreet ___ 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] problem with genion
Hello users, I am carrying a protein simulation using g43a1 force field in gromacs 3.3 i carried out some intial simulation without water in the absence of the neutralizing ions my system was going fine at that time but when i used the genion command to add ions , i found that my protein was broken into parts. i am using genion -s 4min.tpr -o 4min_ion.pdb -nname CL- -nn 6 -g 4min_ion2.log i have checked upto 4min.tpr , structure is fine but only after adding ions i am getting this breakage i.e in the file 4min_ion.pdb what could be the reason for this ? While running the genion it usually asked for the group into which we want to add the ions so i have checked with both the SOL group and OTH group seperatly , in both the cases ions were replacing the solvent molecules. Is their any way by which we can add ions without replacing any solvent molecules ? Thanks With Regards Gurpreet ___ 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] problem regarding freezegrps
Hello Users i am carrying out a dimeric protein simulation with G43a1 force field using Gromacs 3.3 I have added some missing residues into my protein using a seperate program. Now before adding water i want to do some simulation in vaccum to minimized those added resideus and also the hydrogens added via pdb2gmx command. For these i am freezing the protein and crystal waters leaving the added residues so that they can freely move. for that i am using the following input (.mdp) file: title = minimizatio in vaccum integrator = steep dt = 0.002 constraints = none nsteps = 500 nstlist = 10 rcoulomb= 1 rvdw= 1 ns_type = simple coulombtype = PME vdwtype = cut-off pbc = no gen_vel = no freezegrps = protein solvent freezedim = Y Y Y Y Y Y emtol = 100.0 emstep = 0.01 With that i have made an index file where i have mentioned two groups with names 'protein' and 'solvent' but inspite of this i am getting the following problem : Fatal error: Group protein not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. although i have mentioned the index file in the grompp : "aquapo.ndx is the name of index file " grompp -f 1min.mdp -c aquapo_grom.pdb -p aquapo_grom.top -n aquapo.ndx -o 1min.tpr index file used [protein] 1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 26 27 28 29 30 31 32 33 34 35 37 38 39 40 41 42 43 44 45 47 48 49 50 51 52 53 55 56 57 58 59 60 61 64 65 66 67 68 69 70 72 73 74 75 76 77 78 79 80 81 83 85 86 87 88 89 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 110 111 112 113 114 115 116 117 118 119 120 121 122 123 125 126 127 128 129 130 131 132 133 134 136 137 138 139 140 141 142 143 144 146 147 148 149 150 151 152 154 155 156 157 158 159 160 163 164 165 166 167 168 169 171 172 173 174 175 176 177 178 179 180 182 184 185 186 187 188 190 191 192 193 194 195 196 197 198 [solvent] 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 please tell what is the reason for this error waiting for your reply With Regards Gurpreet ___ 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] [Fwd: How simulate two peptides in a box?]
Thanks for the advice In my case no problem is coming while running the grompp, no warning is coming. i could able to generate .tpr file without any error. problem cames only while running the minimization using the .tpr file For convenience, as mention earlier, following was the problem : ... Warning: 1-4 interaction between 1 and 9 at distance 8.443 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file ... could you please suggest me some way out for this. Thanks With Regards Gurpreet On 7/4/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Mark Abraham wrote: >> Thanks Mark for your advice >> >> I tried to run the simulation even by removing all the restraints as you >> told but the same problem was coming. >> In your second reply you asked me to check the topology file. I have a >> doubt in that, actually what are the things i should look at in the >> topology >> file. I have seen my topology file and the related .itp files also but i >> did >> not find anything unusual in that. >> >> Following are the contents of my Topology file: >> >> ; Include forcefield parameters >> #include "ffG43a1.itp" >> >> ; Include chain topologies >> #include "aquapomut_grom_A.itp" >> #include "aquapomut_grom_B.itp" >> >> ; Include water topology >> #include "spce.itp" >> >> #ifdef POSRES_WATER >> ; Position restraint for each water oxygen >> [ position_restraints ] >> ; i funct fcxfcyfcz >>11 1000 1000 1000 >> #endif >> >> ; Include generic topology for ions >> #include "ions.itp" >> >> [ system ] >> ; Name >> Protein in water >> >> [ molecules ] >> ; Compound#mols >> Protein_A 1 >> Protein_B 1 >> SOL71 >> CL- 6 >> SOL 14825 > > Two regions of SOL doesn't sound like a good idea, but I won't swear it's > the problem. this is why I suggested grompp -maxwarn 0, because it will detect the inconsistencies in names and tell you to fix it. > > 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 van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 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] [Fwd: How simulate two peptides in a box?]
Thanks Mark for your advice I tried to run the simulation even by removing all the restraints as you told but the same problem was coming. In your second reply you asked me to check the topology file. I have a doubt in that, actually what are the things i should look at in the topology file. I have seen my topology file and the related .itp files also but i did not find anything unusual in that. Following are the contents of my Topology file: ; Include forcefield parameters #include "ffG43a1.itp" ; Include chain topologies #include "aquapomut_grom_A.itp" #include "aquapomut_grom_B.itp" ; Include water topology #include "spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1 SOL71 CL- 6 SOL 14825 ~ As i told to last time that my protein is a dimer. so my question is this problem is becasue of some missing parameter required for realizing gromacs that its a dimeric protein? with regards Gurpreet On 7/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Hello Gromacs users: Please don't reply to another user's question with a change of topic and not change the subject line of your email. Not doing this means the people who might know the answer for you have no idea in advance what you're going to be asking, and might not bother reading. Best is to start with a new email, not a reply, and to use your subject line sensibly. > I am running a dimeric protein simulation on Gromacs 3.3 using the force > filed G43a1. > > > For initially minimizing the hydrogen i did some small minimization and > equilibration in the vacuum by maintaining the restraints > then i added ions and water but in the very first minimization i m getting > the following error If you want to keep your credibility, when people have already made a suggestion about how to solve your problem, such as I did here http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html, when you post the same problem, you should say what happened when you tried their suggestion. They didn't suggest it for their own entertainment. Look at the minimization "trajectory" and see where things are breaking. Have a look at your topology there, read chapter five thoroughly. 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 ___ 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] [Fwd: How simulate two peptides in a box?]
Hello Gromacs users:
I am running a dimeric protein simulation on Gromacs 3.3 using the force
filed G43a1.
For initially minimizing the hydrogen i did some small minimization and
equilibration in the vacuum by maintaining the restraints
then i added ions and water but in the very first minimization i m getting
the following error
1-4 interaction between 1 and 9 at distance 8.454 which is larger than the
1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
In the log file i am getting :
4 inconsistent shifts check your topology
following is my input file :
title = 1min in water
define = -DPOSRES
integrator = steep
dt = 0.001
constraints = none
nsteps = 500
nstlist = 10
rcoulomb= 1
rlist = 1
rvdw= 1.4
ns_type = grid
coulombtype = PME
pbc = xyz
gen_vel = no
fourierspacing = 0.12
pme_order = 6
ewald_rtol = 1e-5
optimize_fft= yes
comm_mode = angular
emtol = 100.0
emstep = 0.01
after adding the ions i have modified the topology file,
please tell me what is the exact reason for this error or what are the
other things i should check in relation to the error
With regards
Thanks
On 7/2/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Fufeng Liu,
I guess you ran pdb2gmx on the two peptides, where both peptides had
the same chain identifiers. In that case, pdb2gmx will assume that
it's one molecule and connect them. Use chain identifiers to indicate
the different peptides, or build topologies first on separate files
and combine the peptides later.
Cheers,
Tsjerk
On 7/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Please keep requests for help on the list. That way they're archived for
> others to use, and other people can raise points of interest.
>
> The last sentence here
>
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
> is my suggestion for you :-) Probably, you have only one [molecule]
> statement for your two molecules, and by chance you included it first so
> that there was no error message from grompp. If you don't understand why
> this is a problem, find the relevant section of Chapter 5 of the manual
-
> or read the whole lot of that chapter! :-)
>
> Mark
>
> Original Message
> Subject: How simulate two peptides in a box?
> From:[EMAIL PROTECTED]
> Date:Sun, July 1, 2007 11:09 pm
> To: [EMAIL PROTECTED]
>
--
>
> Dear Mark:
> I'm a graduate student at Tianjin University. I want to simulate
two
> peptides
> in a box using GROMACS software? I followed your suggestion
>
> {set up your topologies (suggest one molecule in each of two .itp files)
> #include them in the .top file, pick a starting configuration for both
of
> them in the same structure file, solvate, minimize.}
>
> But when I minimized the system, I got the information ¡±1-4 interaction
> between 83 and 85 at distance 1.862 which is larger than the 1-4 table
> size 1.000 nm¡±. I checked the topology and found that atom 83 belong to
> one peptide and the atom 85 the other peptide. That¡¯s to say the two
> peptides were considered as a peptide. Can you tell me how to do? I'd
be
> very happy and grateful if you could tell me how to do it.
> Looking forward to your reply.
> Best regards.
> Fufeng Liu
>
>
>
>
>
> ___
> 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!
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> www interface or send it to [EMAIL PROTECTED]
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>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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Re: [gmx-users] Re: error during the minimization
thanks for your advice Mr. Manoj I tried the same simulation by taking a structure which was already minimized by another software Amber. Using that structure as the starting structure also, i got the same error i mention earlier. please suggest me something thanks On 6/29/07, M.N. Manoj <[EMAIL PROTECTED]> wrote: It could be an error in protein structure ( because 1 - 9 interaction ), and we usually overcome similar issues by a pre -energy minimization before submitting to gromacs. i m carryin a protein explicit solvent simulation using gromacs 3.3 for intially minimizing the hydrogen i did some small mini and equi in the vaccum by maintaing the restraints then i added ions and water but in the very first minimization i m getting the following error 1-4 interaction between 1 and 9 at distance 8.454 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, in the log file im geting : 4 inconsistant shifts check ur topology following is my input file : title = 1min in water define = -DPOSRES integrator = steep dt = 0.001 constraints = none nsteps = 500 nstlist = 10 rcoulomb= 1 rlist = 1 rvdw= 1.4 ns_type = grid coulombtype = PME pbc = xyz gen_vel = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes comm_mode = angular emtol = 100.0 emstep = 0.01 after adding the ions i have modified the topology file, plz tel me what is the exact reason for this error or what are the other things i should check in relation to the error thanks Gurpreet IIT MADRAS -- M.N. MANOJ PROJECT LEADER - BIOINFORMATICS VITTAL MALLYA SCIENTIFIC RESEARCH FOUNDATION BANGALORE INDIA ___ 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] error during the minimization
Sorry I will take care of this in the future. Thanks for your advice . On 6/29/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > i m carryin a protein explicit solvent simulation using gromacs 3.3 > for intially minimizing the hydrogen i did some small mini and equi in the > vaccum by maintaing the restraints > then i added ions and water but in the very first minimization i m getting > the following error Please use normal capitalization and punctuation and do not invent your own abbreviations and shorthands. You're trying to communicate with busy people whose advice you want for free. To improve your chances of getting useful help, you should make things easy for them, not easy for yourself. If you were still using restraints in this second minimization, try taking them off for a second vacuum geometry optimization phase. > 1-4 interaction between 1 and 9 at distance 8.454 which is larger than the > 1-4 table size 1.000 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > > > in the log file im geting : > > 4 inconsistant shifts check ur topology > > following is my input file : > > title = 1min in water > define = -DPOSRES > integrator = steep > dt = 0.001 > constraints = none > nsteps = 500 > nstlist = 10 > rcoulomb= 1 > rlist = 1 > rvdw= 1.4 > ns_type = grid > coulombtype = PME > pbc = xyz > gen_vel = no > fourierspacing = 0.12 > pme_order = 6 > ewald_rtol = 1e-5 > optimize_fft= yes > comm_mode = angular > emtol = 100.0 > emstep = 0.01 This seems fine. > after adding the ions i have modified the topology file, > plz tel me what is the exact reason for this error or what are the other > things i should check in relation to the error 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 ___ 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] error during the minimization
i m carryin a protein explicit solvent simulation using gromacs 3.3 for intially minimizing the hydrogen i did some small mini and equi in the vaccum by maintaing the restraints then i added ions and water but in the very first minimization i m getting the following error 1-4 interaction between 1 and 9 at distance 8.454 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, in the log file im geting : 4 inconsistant shifts check ur topology following is my input file : title = 1min in water define = -DPOSRES integrator = steep dt = 0.001 constraints = none nsteps = 500 nstlist = 10 rcoulomb= 1 rlist = 1 rvdw= 1.4 ns_type = grid coulombtype = PME pbc = xyz gen_vel = no fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes comm_mode = angular emtol = 100.0 emstep = 0.01 after adding the ions i have modified the topology file, plz tel me what is the exact reason for this error or what are the other things i should check in relation to the error thanks Gurpreet IIT MADRAS ___ 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] PROBLEM REGARDING pdb2gmx & restraints
hello gromacs users my question is regarding the command pdb2gmx which is the first step to process ur input file. i used the force field 43a1 and i m doing some dimeric protein simulation . when i checked the output of the pdb2gmx command i found that this command have not added any hydrogens to the carbon atoms of the protein although to other heavy atoms hydrogens were added. is it the usual behaviour of gromacs or there is some other mistake in giving the command ? pdb2gmx -ff G43a1 -ignh -posrefc 50 -f input.pdb -p toplo.top -o output.pdb-i posre.itp -water spce my second question is about the positional restraints. since i have the dimer so after using the pdb2gmx i got the two posre_A.itp & posre_B.itp files for putting the restriants, i am little bi doubltful about the way we use these files for maintaing the restraints i used in the following way grompp -f input.mdp -c somefile.pdb -p toplo.top -r posre_A.itp,posre_B.itp -o output.tpr is this the right way to mention the restaints or not ? and if i want to change the restraints gradually after each step of the simulation then what is the procedure to do that ? THANKS Gurpreet singh IIT MADRAS ___ 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
