[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 shirt

[gmx-users] broken molecules in ouput of MDRUN

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

[gmx-users] g_sas and PBC

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

[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 > boun

[gmx-users] PROBLEM REGARDING pdb2gmx & restraints

-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 MA

[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 betwe

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

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

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 minimi

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 h

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 : ..

[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 hydrogen

[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 brok

[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 brok

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 W

Re: [gmx-users] problem with genion

'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

[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 s

Re: [gmx-users] question regarding restraints

.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 us

[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

[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 begi

[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

[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-use

[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:

Re: [gmx-users] problem in recognising the atom type

ich 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 fiel