Re: [gmx-users] Hydrogen bonding differences

Thank you Sir for clarifying the confusion. Regards kavya On Fri, Mar 22, 2013 at 11:18 PM, Erik Marklund wrote: > I wouldn't say wrong, but I realized that some residue may make two hbonds > to different parts of the protein, i.e. to the main chain and to a side > chain at the same time. With -

Re: [gmx-users] Proper and improper from other ff?

On 3/22/13 3:14 PM, 라지브간디 wrote: Dear Justin, Actually I've manually added the heme -ligand parameters details such as bond, angle and dihedral to my topology created by pdb2gmx via gromos43a1. ( Those manually added parameters details are taken from charmm and amber ff, which are availabl

[gmx-users] Proper and improper from other ff?

Dear Justin, Actually I've manually added the heme -ligand parameters details such as bond, angle and dihedral to my topology created by pdb2gmx via gromos43a1. ( Those manually added parameters details are taken from charmm and amber ff, which are available in some published articles ). I co

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

Hi, Actually, if you don't want to run across the network, with those Westmere processors you should be fine with running OpenMP across the two sockets, i.e mdrun -ntomp 24 or to run without HyperThreading (which can be sometimes faster) just use mdrun -ntomp 12 -pin on Now, when it comes to GPU

Re: [gmx-users] Hydrogen bonding differences

I wouldn't say wrong, but I realized that some residue may make two hbonds to different parts of the protein, i.e. to the main chain and to a side chain at the same time. With -merge this counts as one if you analyze the entire protein. If you split your analysis such hbonds will show up in

Re: [gmx-users] how can we obtain replicated trajectory?

On Fri, Mar 22, 2013 at 3:54 PM, Albert wrote: > On 03/22/2013 03:45 PM, Mark Abraham wrote: > >> As you can see in your plot, no replicas from 400K got down to 300K in the >> 1.5ns you simulated. So you've so far derived no benefit from REMD (unless >> you want sampling at lots of temperatures).

Re: [gmx-users] Hydrogen bonding differences

Sir, I tried -nomerge. It is fine now. But will it be wrong to calculate without nomerge option? Thank you Kavya On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund wrote: > I could see how -merge (on by default) could lead to this. Have you tried > -nomerge? > > Erik > > > On Mar 22, 2013, at 4:46

Re: [gmx-users] proper and improper dihedrals in topology file from other ff

On 3/22/13 9:18 AM, 라지브간디 wrote: Dear Justin, I got understand the gromos ff improper style. however, what i am asking here is how would i use the charmm/amber improper from literuatre where they indicate the improper in this was ( something X-X) Improper CPB-X-X-CR1E 90.0 0.0 CC - X-X

Re: [gmx-users] Hydrogen bonding differences

I could see how -merge (on by default) could lead to this. Have you tried -nomerge? Erik On Mar 22, 2013, at 4:46 PM, Kavyashree M wrote: Dear Users, As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. Still the Total intra-protein hydrogen bonds is not equal (MM +MS

Re: [gmx-users] Hydrogen bonding differences

Dear Users, As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds. Still the Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond. Is there any other solution? Thank you Kavya On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M wrote: > Dear Sir, > > Sure I wi

Re: [gmx-users] how can we obtain replicated trajectory?

On 03/22/2013 03:45 PM, Mark Abraham wrote: As you can see in your plot, no replicas from 400K got down to 300K in the 1.5ns you simulated. So you've so far derived no benefit from REMD (unless you want sampling at lots of temperatures). Perhaps a simulation a hundred times longer might get a few

Re: [gmx-users] how can we obtain replicated trajectory?

As you can see in your plot, no replicas from 400K got down to 300K in the 1.5ns you simulated. So you've so far derived no benefit from REMD (unless you want sampling at lots of temperatures). Perhaps a simulation a hundred times longer might get a few such events? You might as well have run a sim

Re: [gmx-users] Error in REMD

This would normally mean you are somehow calling code from one GROMACS version with code from another. Some kind of dynamic library loading mishap? Mark On Fri, Mar 22, 2013 at 10:41 AM, Nikunj Maheshwari < nixcrazyfor...@gmail.com> wrote: > Dear all... > > We ran REMD simulations for 36 replica

Re: [gmx-users] Re: Re: help with chromophore of a GFP

On Fri, Mar 22, 2013 at 2:36 PM, Anna MARABOTTI wrote: > > Dear Mark, Justin and other gmx-users, > thank you very much for your > help. Thanks to your suggestions, I made some steps forward, but still I > don't see the end of my travel... > > First of all, I would like to say > that my previou

[gmx-users] Re: Re: help with chromophore of a GFP

Dear Mark, Justin and other gmx-users, thank you very much for your help. Thanks to your suggestions, I made some steps forward, but still I don't see the end of my travel... First of all, I would like to say that my previous problem was solved when I renamed O1 to OA. Justin was right. When I

[gmx-users] proper and improper dihedrals in topology file from other ff

Dear Justin, I got understand the gromos ff improper style. however, what i am asking here is how would i use the charmm/amber improper from literuatre where they indicate the improper in this was ( something X-X) Improper > CPB-X-X-CR1E 90.0 0.0 > CC - X-X-NB 18.3 0.0 > What X sh

[gmx-users] how can we obtain replicated trajectory?

Hello: I've finished a replica exchange simulation with 72 replica (300K-580K) under explicit solvent model. It generate 72 trajectory and the replica since to "cross" well with neighboring temperature. Here is the figure: http://dl.dropbox.com/u/56271062/REMD.png I am just wondering how

Re: [gmx-users] Mismatching number of PP MPI processes and GPUs per node

Hello Szilard Many thanks for these very useful comments! We run jobs on a single node of a small Apple cluster (no Infiniband unfortunately). One node has two Intel(R) Xeon(R) X5650 Processors each with 6 cores and 12 threads, so in total 12 cores and 24 threads. I have compiled GROMACS 4.6.1 w

[gmx-users] Error in REMD

Dear all... We ran REMD simulations for 36 replicas. We got an error which stopped the whole simulation. " Reading file md21.tpr, VERSION 4.5.5 (single precision) Loaded with Money Reading file md24.tpr, VERSION 4.5.5 (single precision) Loaded with Money ---