Re: [gmx-users] forcefield error for atoms

Thanks Justin! my system is a CNT but I need to insert some atoms in it with no bonds. The best way I found is to make a .pdb and .gro files of the newly constructed system and then without the use of g_x2top command, I added anything needed to the .top file which was made previously without the

[gmx-users] simultaneous runs

Dear all, I performed 2 runs one after the other. Then, I performed those 2 runs simultaneously(no special commands were applied, I just used different terminals with mdrun -v command) but in different directories. Results (like msd and energies) were expected to be nearly the same. but they are

[gmx-users] there wasn't md_0_1.xtc file

Hi every body after creating a covalent bond, I ran output file based on GROMACS tutorial (Lysozyme in water) and applied the following command mdrun -deffnm md_0_1. at the end of 1ns, I achieved the following output files: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log md_0_1.tpr md_0_1.trr

[gmx-users] the study of concentration effect in gromacs

Dear Tsjerk thanks for your advice you mean , if i do my simulation in cubic box (1*1*1 nm3)... Now, for twice of concentration, i should simulate for example in cubic box (0.5*0.5*0.5 nm3)? or for instance, i simulated on a system using *2i30* pdb file (Aspirin+Salicilic Acid) that including

Re: [gmx-users] there wasn't md_0_1.xtc file

On 4/4/15 1:45 PM, marzieh dehghan wrote: Hi every body after creating a covalent bond, I ran output file based on GROMACS tutorial (Lysozyme in water) and applied the following command mdrun -deffnm md_0_1. at the end of 1ns, I achieved the following output files: md_0_1.cpt md_0_1.edr

Re: [gmx-users] the study of concentration effect in gromacs

Hi Elham, No, a box of 0.5*0.5*0.5 has 0.125 times the volume of one of 1*1*1, so gives an 8 times as high concentration. But it gets more complicated if you mean the concentration of the solution around a protein. I tend to favour using molality (as mol solute per mol solvent) for that. Yes,