[gmx-users] LINCS warning

Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and

[gmx-users] Gromacs version

Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Thanks in advance, Regards, Raghu ** Y. M. Ragothaman, Research Scholar, Centre for Computational Biology and

Re: [gmx-users] LINCS warning

Dear all, I have a query, 1. Are two trajectories comparable if each one of them has been run in a different version of gromacs? Eg, v3.2 and v3.3. Define comparable. If you mean are they sampling the same thermodynamic ensemble, then the answer is yes if you used the same algorithms. If you

Re: [gmx-users] Gromacs version

I think the statistical reserves but the two trajectories are not exactly the same. On 9/9/06, Ragothaman Yennamalli [EMAIL PROTECTED] wrote: Dear all,I have a query,1. Are two trajectories comparable if each one of themhas been run in a different version of gromacs? Eg, v3.2 and v3.3.Thanks in

Re: [gmx-users] problem with dimer simulation !

try - cluster, and then as cluster group protein.Kay.On Sep 9, 2006, at 11:09 AM, C.W. Liang wrote: hi, all user:   i performed the dimer simulation,  and want to realize the interaction between two peptides. but frequently, i  encountered this kind of problem:  sometimes peptides moved out of the

[gmx-users] May I use -b and -e in the cosine con tent calculation of PC?

Hi dear friends, I just made an essential dynamics of 5ns; I calculated the cosine content of PC1 byusing g_analyze -f proj5ns.xvg -cc proj5ns_cc.xvg it gave: "Cosine content of set 1 with 0.5 periods: 0.749969" the valueis rather too high. However, I foundthat only trajectorybetween 3300~3890