Re: [gmx-users] Re: Multiple protein simulations in a box

Hi Rajeswari, try this really interesting work done by De Simone et al. and published recently on PNAS. http://www.pnas.org/content/109/18/6951.full Hope this helps. Cheers, Davide Davide Mercadante Ph.D. School of Chemical Sciences The University of Auckland Auckland New Zealand On 3/

[gmx-users] Re: Multiple protein simulations in a box

Thank you Rama and Justin for ur kind reply. @Justin: May i request you to kindly direct me to some references of multiple protein simulation in a box using standard MD? And i have seen the tutorial about multi protein simuation is under development. May i know when can we expect it to be ready? O

Re: [gmx-users] Re: Re,I have a problem with my biphasic system

On 11/2/12 3:11 PM, Ali Alizadeh wrote: Dear Justin In your opinion, when g_density represent density profiles, this profile is related to particles; but what are the particles? Atoms or Residues? i think that we determine type of particles in .ndx, is it true? If i want to represent propane

Re: [gmx-users] a question related to tpbconv and trjcat

On 11/2/12 10:00 PM, Acoot Brett wrote: Dear All First I ran a 5 ns MD (md-0ns-5ns), I get md-0ns-5ns.tpr and md-0ns-5ns.cpt,then I extend it for 1 ns by tpbconv -s tpbconv -s md-0ns-5ns.tpr -extend 1000 -o md-5ns-to-6ns.tpr mdrun -deffnm md-5ns-to-6ns -cpi md-0ns-5n.cpt Then I further ext

[gmx-users] a question related to tpbconv and trjcat

Dear All First I ran a 5 ns MD (md-0ns-5ns), I get md-0ns-5ns.tpr and md-0ns-5ns.cpt,then I extend it for 1 ns by tpbconv -s tpbconv -s md-0ns-5ns.tpr -extend 1000 -o md-5ns-to-6ns.tpr mdrun -deffnm md-5ns-to-6ns -cpi md-0ns-5n.cpt Then I further extend it for 2 ns by tpbconv -s md-5ns-to-6

Re: [gmx-users] Re: are wall atoms virtual ?

Wall atoms are virtual in the sense that they are just special Z-axis boundary conditions based on the integration of the LJ potential parameterized by the atom type, integraton model, and specified density of the "wall". The particles don't physically exist so you will not see them in VMD (becau

[gmx-users] g_rms/rmsf: fit vs. nofit

Hi I have sort of a noob question about when to fit and when not to fit when computing rmsd and rmsf. My use-case is to look at the motion of different domains of a protein where there are atoms near the COM of the starting structure that remain relatively stable throughout the simulation accor

[gmx-users] Setting up a complex membrane simulation

Whatever method you use to set up your system, and be it atomistic or coarse-grained, I suggest that you build at least 2 such systems independently and run them all for the same amount of time. Looking at convergence from the same starting structure with different initial velocities is not nea

Re: [gmx-users] Re: why it is so slow

On 11/2/12 12:54 PM, Albert wrote: On 11/02/2012 05:48 PM, Justin Lemkul wrote: That system is not small, it's rather large. Are you sure each replica is really running on 24 processors? It occurred to me that there was a problem in 4.5.4 that was fixed for 4.5.5, but the "fix" was really ju

Re: [gmx-users] Re: why it is so slow

I did not follow your previous discussion, but I am sure you need to quantitatively estimate the slowness of your simulation. For instance, you can compute the factor by dividing the execution time using GBSA by the execution time for protein in vacuum. The people often complain it is slow, where

Re: [gmx-users] Re: why it is so slow

On 11/02/2012 05:48 PM, Justin Lemkul wrote: That system is not small, it's rather large. Are you sure each replica is really running on 24 processors? It occurred to me that there was a problem in 4.5.4 that was fixed for 4.5.5, but the "fix" was really just a workaround, allowing a maximum

Re: [gmx-users] Re: Re,I have a problem with my biphasic system

On 11/2/12 11:48 AM, Ali Alizadeh wrote: Dear Justin I wanted to check that Did i simulate? I said if i multiplied average number density(from each part of profile) to volume and summation of them was nearly number of my total number of particle, i can say my simulation is correct, I did it

Re: [gmx-users] Setting up a complex membrane simulation

Hi Jonas, Do you mean atomistic or coarse grained? Of course you should mean coarse grained as it's out of the question to reach equilibration for a significant amount of lipids with such complexity, which will take several microseconds. I have a tool for building membranes, which could be of valu

Re: [gmx-users] Re: why it is so slow

On 11/2/12 12:23 PM, Albert wrote: Hello Vitaly: thanks a lot for kind comments. Do you have any idea why the running is so slow? Especially considering it is with GBSA model and my protein is only with 240 aa. That system is not small, it's rather large. Are you sure each replica is real

Re: [gmx-users] Re: why it is so slow

Hello Vitaly: thanks a lot for kind comments. Do you have any idea why the running is so slow? Especially considering it is with GBSA model and my protein is only with 240 aa. thank you very much best Albert On 11/02/2012 04:30 PM, Dr. Vitaly Chaban wrote: If I turn this option on, such as:

[gmx-users] Total energy for a group of molecule

Dear experts, This question has been asked several times before but so far it remains unanswered. I would like to calculate the total energy (kinetic plus potential) for a group of molecules. In my case, I would like to look at certain water molecules. So far, I know that I can get the kinetic en

[gmx-users] Re: why it is so slow

>> If I turn this option on, such as: >> >> pcouple=Isotropic >> >> it is said: >> >> >> ERROR 1 [file eq.mdp, line 78]: >>Pressure coupling not enough values (I need 1) >> >> >> WARNING 1 [file eq.mdp]: >>Turning off pressure coupling for vacuum system You canNOT use pressure coupling

Re: [gmx-users] Setting up a complex membrane simulation

On 11/2/12 11:15 AM, jonas87 wrote: Dear all, I wish to run a simulation of a membrane consisting of about 10 different lipids. Through the automated topology builder ( example ) I can obtain of each lipid a structure file in pdb fo

[gmx-users] Setting up a complex membrane simulation

Dear all, I wish to run a simulation of a membrane consisting of about 10 different lipids. Through the automated topology builder ( example ) I can obtain of each lipid a structure file in pdb format (it has one single molecule) and an

Re: [gmx-users] why it is so slow

On 11/2/12 11:08 AM, Albert wrote: On 11/02/2012 04:02 PM, Justin Lemkul wrote: I wasn't suggesting that you use NPT, I was merely pointing out that you made an statement that wasn't true and thought I would mention it. It looks like you have other issues to deal with. -Justin Hello Just

Re: [gmx-users] why it is so slow

On 11/02/2012 04:02 PM, Justin Lemkul wrote: I wasn't suggesting that you use NPT, I was merely pointing out that you made an statement that wasn't true and thought I would mention it. It looks like you have other issues to deal with. -Justin Hello Justin: thanks a lot for such kind rep

Re: [gmx-users] Pull code, Velocity distribution

On 11/2/12 10:52 AM, Samadashvili Nino wrote: Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pu

Re: [gmx-users] why it is so slow

On 11/2/12 10:56 AM, Albert wrote: On 11/01/2012 06:15 PM, Justin Lemkul wrote: On 11/1/12 12:55 PM, Albert wrote: hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. Based on your .mdp file, you're not

Re: [gmx-users] why it is so slow

On 11/01/2012 06:15 PM, Justin Lemkul wrote: On 11/1/12 12:55 PM, Albert wrote: hello: I am running a 40ns REMD with GBSA solvent NPT simulations. It is exchange for 16 different temperature with exchange step 300. Based on your .mdp file, you're not doing NPT (pcoupl = no). Hello J

[gmx-users] Pull code, Velocity distribution

Hello, I have been using the pull code for friction calculations. I am not doing umbrella sampling but just pulling one slab of crystal on top of another with the constant velocity. I would like to know how Gromacs is calculating the pulling force (pullf.xvg) during sliding. Is the pul

Re: [gmx-users] cosine content and nonconverged trajectory

On 11/2/12 8:17 AM, ahmet yıldırım wrote: Dear users, The cosine content of the principal components is an effective indicator for predicting whether or not a trajectory has been convergent. A high cosine content typically indicates a nonconverged trajectory (Chapter 5: Normal Modes and Essent

[gmx-users] cosine content and nonconverged trajectory

Dear users, The cosine content of the principal components is an effective indicator for predicting whether or not a trajectory has been convergent. A high cosine content typically indicates a nonconverged trajectory (Chapter 5: Normal Modes and Essential Dynamics Steven Hayward and Bert L. de Gro

Re: [gmx-users] Re,I have a problem with my biphasic system

On 11/2/12 6:46 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply; I'm reproducing this paper that related to this topic, dx.doi.org/10.1088/0953-4075/42/3/035302 It's title : A molecular dynamic study of water/methane/propane I only had time to quickly look at this paper, but it i

Re: [gmx-users] about tc_grps in mdp file...

thank you.. On Fri, Nov 2, 2012 at 3:56 PM, Justin Lemkul wrote: > > > On 11/2/12 1:13 AM, rama david wrote: > >> Dear all, >> I am running a system with sol 40646 atom and ion, NA 629 CL 634. >> At the time of nvt and npt should i have to make different *tc_grps* for >> >> ion and sol or sho

Re: [gmx-users] Re,I have a problem with my biphasic system

On 11/2/12 3:25 AM, Ali Alizadeh wrote: Dear Justin Thank you for your reply. I'm studying hydrate formation, my temprature and pressure are 240 k and 300 bar, Has anyone ever demonstrated that you can observe such phenomena in an MD simulation under these conditions? Also note that you

Re: [gmx-users] Re: Why potential energy not in negative value?

On 11/1/12 8:25 PM, shika wrote: Hi Justin, Thanks for your explaination..First of all i got the HFIP topology from this site which prof Alan give it to me compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files Due to before this when i create the structure by using packmol and run it usi

Re: [gmx-users] T - Annealing at NP - cell expands

On 11/1/12 5:06 PM, Steven Neumann wrote: On Thu, Nov 1, 2012 at 8:45 PM, Justin Lemkul wrote: On 11/1/12 4:36 PM, Steven Neumann wrote: Dear Gmx Users, I have system with protein in water. I equlibrated it in at 300 K and 1 bar for 5 ns with position restrained of protein heavy atoms. I

Re: [gmx-users] About BoxVector and APL

On 11/1/12 11:20 PM, vidhya sankar wrote: As uou Told me in the Previous Mail I have Given My sereis of Commands With Real file Names ./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -ignh -ter -water spc ./editconf_d -f 2KDQ.gro -o 2KDQ_newbox.gro -box 6 6 6 -c ./editconf_d -f dppc128.pdb -o dppc

Re: [gmx-users] about tc_grps in mdp file...

On 11/2/12 1:13 AM, rama david wrote: Dear all, I am running a system with sol 40646 atom and ion, NA 629 CL 634. At the time of nvt and npt should i have to make different *tc_grps* for ion and sol or should be make one group Nonprotein ( these include sol + ion)..these is default. http:/

Re: [gmx-users] Multiple protein simulations in a box

On 11/2/12 5:52 AM, Rajeswari A. wrote: Dear Gromacs Users, I want to simulate multiple number of proteins in a box. I am very confused in choosing what MD method will be useful to solve my problem. Can i do it with regular molecular dynamics simulations? I am not sure whether diffusion of solu

Re: [gmx-users] Free energy calculations with BAR and TI

Hi Fernandez, Actually, this is a known problem. You should find the description and solution in the archive. I had the same problem, so this may make your search more easy :) The problem is in the code, at some point float and numbers are messed up, or something in this direction. You can

Re: [gmx-users] Multiple protein simulations in a box

Dear Rajeswari, May I ask you why you want to do the multiple protein simulation.?? Please mention the purpose clearly, otherwise it is hard to understand what you are doing and what you need???, With best wishes and Regards, Rama David On Fri, Nov 2, 2012 at 3:22 PM, Rajeswari A. wrote: > De

Re: [gmx-users] Simulation of charged systems (2)

From what I remember from my earlier impressions ... the equations are not correct when the system is not neutral. In your case the charge is significantly high ... On Nov 2, 2012, at 9:36 AM, Felipe Pineda, PhD wrote: Hi, I recently sent a query, but it was probably not appealing enoug

[gmx-users] Free energy calculations with BAR and TI

Hi all, Can I use the same simulations (with delta_lambda=0, init_lambda and foreign_lambda) for TI and BAR calculations? I guess that boils down to whether the simulations with foreign_lambda are in equilibrium with the init_lambda, or they are some sort of hybrid ensemble between the differen

[gmx-users] Simulation of charged systems (2)

Hi, I recently sent a query, but it was probably not appealing enough to get some feedback. So I try again with a shorter one: Is there any theoretical or technical objection against running an NPgammaT simulation on a charged (total charge = -36) membrane model (hydrated bipolar monolayer)