Re: [gmx-users] Replica exchange shell script

Sukit Leekumjorn wrote: Thank you very much Mark I got REMD to run now but I ended up having the same problem as the other users had in the past. Below is the error message. I got this to run for 2 nodes. For 4, 6, and 8 nodes, the below error shows up in the log files. I did try several

Re: [gmx-users] Replica exchange shell script

Thank you very much Mark I got REMD to run now but I ended up having the same problem as the other users had in the past. Below is the error message. I got this to run for 2 nodes. For 4, 6, and 8 nodes, the below error shows up in the log files. I did try several suggestions from the mail

[gmx-users] g_sas -or

Hi: I am using the g_sas with the -or option . The output file have 3 colums: first the res number, second the sasa value, third I dont know. To what corresponds the third columnin the file? Best regards Anthony - Antes ahora

Re: [gmx-users] Analysis programs and PBC.

Dear Maxim, dear David, On Sun, 2006-02-26 at 22:34 +0100, David van der Spoel wrote: > Maxim Fedorov wrote: > > Dear all, > > > > I have been successfully using Gromacs for a couple years without > > bothering you - > > manual + reading the mailing list was completely enough. > > > > But … th

Re: [gmx-users] LINCS warning in Position Restraint

Hi Om Prakash, The warnings below are serious indicators of trouble and should never be ignored. It says that you're using the wrong .top file and .gro file together. Apparently, in one you have the cl- ions and in the other you haven't. As a consequence of the resulting shift the whole connectivit

[gmx-users] Counterions: influence on protein dynamics.

Dear all, I am doing MD simulations of some polypeptide chains. These polypeptides have non-zero net charge; therefore, I should add some counterions into the box to use the PME. I am wondering – is there an elegant way to reduce influence of these counterions on polypeptide dynamics? Until now

Re: [gmx-users] Analysis programs and PBC.

Maxim Fedorov wrote: Dear all, I have been successfully using Gromacs for a couple years without bothering you - manual + reading the mailing list was completely enough. But … this is the second mail for this afternoon. The question is: are there any analysis programs in GROMACS package whi

[gmx-users] Analysis programs and PBC.

Dear all, I have been successfully using Gromacs for a couple years without bothering you - manual + reading the mailing list was completely enough. But … this is the second mail for this afternoon. The question is: are there any analysis programs in GROMACS package which are sensitive to Peri

[gmx-users] LINCS warning in Position Restraint

Hi all, I am trying to position restraint on 1OMB.pdb using gromacs 3.2 I have included 2 CL- ion. My *.top is after editing: [ molecules ] ; Compound#mols Protein 1 SOL 1768 CL- 2 Am doing

Re: [gmx-users] genbox fatal error with ligand-receptor complex: realloc for atoms_solvt->atomname : No such file or directory

Shanjie Huang wrote: Hi, I am working on a molecular dynamics of a receptor-ligand complex. I created the .gro files for receptor and ligand separatedly and merged them together, making sure the atom numbers are continuous. In the .top file of receptor I have put " #include "ligand.itp" " and app

[gmx-users] genbox fatal error with ligand-receptor complex: realloc for atoms_solvt->atomname : No such file or directory

Hi, I am working on a molecular dynamics of a receptor-ligand complex. I created the .gro files for receptor and ligand separatedly and merged them together, making sure the atom numbers are continuous. In the .top file of receptor I have put " #include "ligand.itp" " and append a line for ligand i