- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Wed, 23 Nov 2016 08:02:42 -0500

Hi,

On Wed, Nov 23, 2016 at 4:52 AM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:

*> I’ll get the velocities from the output restart file and use them with the set of coordinates I’ve chosen even if they don’t exactly match the ones in the restart output file (hoping this won’t cause much trouble).
*

I think that you'll probably get a reasonable velocity distribution if

you set irest=0 and tempi to your target temperature instead (and it

will be less work).

*> I’ll use the trajin/out commands from now on. I had figured that cpptraj would be faster than me in finding in which fragment of the trajectory frame 3089 would be. I had to figure it out again by myself anyway in order to use the closest corresponding velocities.
*

Just to be clear, 'trajin' and 'trajout' *are* cpptraj commands. The

difference is that the 'loadcrd' command loads the trajectories into

memory as a COORDS data set, while 'trajin' keeps them on the disk.

Loading coordinates into memory can make sense if you're going to want

to access them many times (e.g. when performing cluster analysis,

calculating PCs, etc.) but if all you want is a single pass over your

coordinates (or a single frame) the 'trajin' command makes more sense.

Hope this clears things up,

-Dan

*>
*

*> Thank you again for all the information,
*

*>
*

*> Ruth
*

*>
*

*>> On 22 Nov 2016, at 19:28, Daniel Roe <daniel.r.roe.gmail.com> wrote:
*

*>>
*

*>> Hi,
*

*>>
*

*>> Amber trajectory files do not contain velocities by default, so any
*

*>> restart written from a trajectory frame will also not contain velocity
*

*>> information. Start your MD run with 'irest = 0'.
*

*>>
*

*>> If you do have velocity information in your trajectory files, it
*

*>> should be included in the output restart - make sure you're using the
*

*>> latest version of cpptraj.
*

*>>
*

*>> Also note that you don't have to load all of your trajectories in
*

*>> memory to extract a single frame (in fact it's very inefficient to do
*

*>> so). Just use 'trajin' instead of 'loadcrd' and 'trajout' instead of
*

*>> 'crdout' (specifying 'onlyframes' instead of 'crdframes'), e.g.
*

*>>
*

*>> parm native2.parm
*

*>> trajin nat2_md-qm.nc name nat2-0
*

*>> ...
*

*>> trajout nat2-0 nat2-0_3089.rst restart onlyframes 3089
*

*>>
*

*>> Hope this helps,
*

*>>
*

*>> -Dan
*

*>>
*

*>> On Tue, Nov 22, 2016 at 12:21 PM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
*

*>>> Dear Amber users,
*

*>>>
*

*>>> I’ve been performing QM/MM molecular dynamics of a protein and its ligand. Afterwards, I’ve run cluster analysis to identify representative structures and continue the calculations from one of these structures.
*

*>>>
*

*>>> In order to do so, I’ve extracted the coordinates of the structure I’ve chosen using the following script in cpptraj:
*

*>>>
*

*>>> #Load topology and trajectories
*

*>>> parm native2.parm
*

*>>> loadcrd nat2_md-qm.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm1.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm2.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm3.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm4.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm5.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm6.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm7.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm8.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm9.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm10.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm11.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm12.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm13.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm14.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm15.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm16.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm17.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm18.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm19.nc name nat2-0
*

*>>> loadcrd nat-ew2-0_mdqm20.nc name nat2-0
*

*>>> crdout nat2-0 nat2-0_3089.rst restart crdframes 3089,3089
*

*>>>
*

*>>> Now that I want to pursue the QM/MM MD adding new residues to the QM region using the restart coordinates obtained with cpptraj and the topology file I was using from the beginning of my calculation, I get the following error message:
*

*>>>
*

*>>> ERROR: I could not find enough velocities in
*

*>>> nat2-0_3089.rst
*

*>>>
*

*>>> I guess I’ve made a mistake somewhere (as I’ve never extract coordinates using cpptraj), please help me correct it to continue my simulation.
*

*>>>
*

*>>> Thanks in advance,
*

*>>>
*

*>>> Ruth
*

*>>>
*

*>>> _______________________________________________
*

*>>> AMBER mailing list
*

*>>> AMBER.ambermd.org
*

*>>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>
*

*>>
*

*>>
*

*>> --
*

*>> -------------------------
*

*>> Daniel R. Roe
*

*>> Laboratory of Computational Biology
*

*>> National Institutes of Health, NHLBI
*

*>> 5635 Fishers Ln, Rm T900
*

*>> Rockville MD, 20852
*

*>> https://www.lobos.nih.gov/lcb
*

*>>
*

*>> _______________________________________________
*

*>> AMBER mailing list
*

*>> AMBER.ambermd.org
*

*>> http://lists.ambermd.org/mailman/listinfo/amber
*

*>>
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

Date: Wed, 23 Nov 2016 08:02:42 -0500

Hi,

On Wed, Nov 23, 2016 at 4:52 AM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:

I think that you'll probably get a reasonable velocity distribution if

you set irest=0 and tempi to your target temperature instead (and it

will be less work).

Just to be clear, 'trajin' and 'trajout' *are* cpptraj commands. The

difference is that the 'loadcrd' command loads the trajectories into

memory as a COORDS data set, while 'trajin' keeps them on the disk.

Loading coordinates into memory can make sense if you're going to want

to access them many times (e.g. when performing cluster analysis,

calculating PCs, etc.) but if all you want is a single pass over your

coordinates (or a single frame) the 'trajin' command makes more sense.

Hope this clears things up,

-Dan

-- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Nov 23 2016 - 05:30:02 PST

Custom Search