Dear Amber Users,
I have download the latest Amber24 and AmberTools24.
I'm going to install them to my new workstation with the OS Ubuntu 22.04.
I would like to ask that if you have the procedures for installing because I'm not familia with this operating system.
Thank you very much.
Yuan
At 2024-11-08 04:00:01, amber-request.ambermd.org wrote:
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>AMBER Mailing List Digest
>
>Today's Topics:
>
> 1. Question about cpptraj for PBC removal (Enrico Martinez)
> 2. Re: Question about cpptraj for PBC removal (Daniel Roe)
> 3. Re: Atommap doesn't change atom names (Daniel Roe)
> 4. Re: Question about cpptraj for PBC removal (Enrico Martinez)
> 5. Re: Question about cpptraj for PBC removal (Daniel Roe)
> 6. Re: Question about cpptraj for PBC removal (Enrico Martinez)
> 7. Re: Question about cpptraj for PBC removal (Daniel Roe)
> 8. Re: Question about cpptraj for PBC removal (Enrico Martinez)
> 9. Re: Question about cpptraj for PBC removal (Enrico Martinez)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Thu, 7 Nov 2024 09:36:46 +0100
>From: Enrico Martinez <jmsstarlight.gmail.com>
>To: AMBER Mailing List <amber.ambermd.org>
>Subject: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAALQopwN+14QC+6PXc9tY6-RSyzvzxtAtF2EhNR=tBM4fhwUUA.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Dear Amber users !
>
>I still have a question about removing the periodic boundary conditions
>(PBC) from membrane simulations. I used the autoimage command in cpptraj,
>and it works well for keeping the protein centered in the box. However,
>some lipids occasionally appear to rapidly jump back and forth across the
>box boundaries, even over several nanoseconds, creating an unrealistic
>effect in the membrane. Is there a way to fix this visual artifact with
>additional options in cpptraj?
>
>Many thanks in advance
>
>Enrico
>
>
>------------------------------
>
>Message: 2
>Date: Thu, 7 Nov 2024 08:23:20 -0500
>From: Daniel Roe <daniel.r.roe.gmail.com>
>To: Enrico Martinez <jmsstarlight.gmail.com>, AMBER Mailing List
> <amber.ambermd.org>
>Subject: Re: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAAC0qOYKE8J9Ezvvak3tjV+EchE+06-qO9ckv5chJbiQyM+ubA.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Thu, Nov 7, 2024 at 3:37?AM Enrico Martinez via AMBER
><amber.ambermd.org> wrote:
>> I still have a question about removing the periodic boundary conditions
>> (PBC) from membrane simulations. I used the autoimage command in cpptraj,
>> and it works well for keeping the protein centered in the box. However,
>> some lipids occasionally appear to rapidly jump back and forth across the
>> box boundaries, even over several nanoseconds, creating an unrealistic
>> effect in the membrane. Is there a way to fix this visual artifact with
>> additional options in cpptraj?
>
>First, just to be clear the 'autoimage' command isn't removing
>periodic boundary conditions, it's just removing the "jumps" that
>happen due to wrapping when PBCs are present.
>
>Membranes are tricky since you want the lipids "anchored", but the
>current algorithm is really best suited to dilute systems. I added the
>'moveanchor' keyword for 'autoimage' specifically to try to address
>these kinds of systems; essentially it makes the anchor the previous
>molecule. I've had success with it for membrane systems, but you
>should definitely test it with the problematic frames you are seeing
>before trying it on your whole trajectory. If you still have issues
>please try to send me off list the topology and the problematic frames
>(or if possible the entire trajectory) and I'll see what I can do.
>
>Hope this helps,
>
>-Dan
>
>
>
>------------------------------
>
>Message: 3
>Date: Thu, 7 Nov 2024 08:44:12 -0500
>From: Daniel Roe <daniel.r.roe.gmail.com>
>To: Maciej Spiegel <maciej.spiegel.umw.edu.pl>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Atommap doesn't change atom names
>Message-ID:
> <CAAC0qOZccr3mgP5+5Gn6+1TZWkfWpHh=rXKqjYne3NGmCKOGTw.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>Thanks for providing the files.
>
>On Tue, Nov 5, 2024 at 7:55?AM Maciej Spiegel <maciej.spiegel.umw.edu.pl> wrote:
>>
>> This fails and mapped.mol2 has atom names of charges.mol2, despite atommap.dat output indicates they are recognized correctly. The files:
>
>Actually, you can see from the atommap output that you provided that
>some of the atoms were not mapped:
>
>> 35 H11 35 H
>> 36 H12 36 H
>> 37 H13 37 H
>> --- --- 38 C
>> --- --- 39 H
>> --- --- 40 H
>> --- --- 41 H
>> 38 Cl1 42 Cl
>
>This is because charges.mol2 contains 3 fewer atoms than A8C.pdb.
>Since 'changenames' requires that all atoms have been mapped, this is
>why no names are changed. Maybe I should add a flag allowing any
>mapped atom names to be changed.
>
>Also, it seems like you may have reversed the order of target and
>reference to 'atommap' - do you really want A8C.pdb to be the
>reference? It has generic atom names:
>
>> HETATM 33 O 0 0.887 0.876 -0.201 O
>> HETATM 34 C 0 0.046 0.947 -1.356 C
>> HETATM 35 H 0 -0.762 0.254 -1.252 H
>> HETATM 36 H 0 -0.345 1.939 -1.452 H
>> HETATM 37 H 0 0.616 0.703 -2.228 H
>
>which will cause problems if you try to build with it (since all atom
>names in a residue must be unique).
>
>I'll let you know if I can get around to implementing name changes
>with partial atom maps. In the meantime if you know there are atoms
>you do not want mapped you could always remove them from A8C.pdb to
>get the atoms in target and reference to match up.
>
>Hopefully this clears some things up.
>
>-Dan
>
>
>
>------------------------------
>
>Message: 4
>Date: Thu, 7 Nov 2024 14:52:59 +0100
>From: Enrico Martinez <jmsstarlight.gmail.com>
>To: Daniel Roe <daniel.r.roe.gmail.com>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAALQopz55muR96OWVwov9epu6FG4FWFRSccBCNHE3reLtYgP3Q.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Thank you very much Daniel !
>I am going to test it and will report you the results ..
>One question: may I use the option 'moveanchor' with another command of
>ccptraj: image center familiar
>Sometimes it works better for membrane protein system producing the system
>oriented in the center of the membrane ( but still with lipid jumps)
>
>Enrico
>
>Il giorno gio 7 nov 2024 alle ore 14:23 Daniel Roe <daniel.r.roe.gmail.com>
>ha scritto:
>
>> Hi,
>>
>> On Thu, Nov 7, 2024 at 3:37?AM Enrico Martinez via AMBER
>> <amber.ambermd.org> wrote:
>> > I still have a question about removing the periodic boundary conditions
>> > (PBC) from membrane simulations. I used the autoimage command in cpptraj,
>> > and it works well for keeping the protein centered in the box. However,
>> > some lipids occasionally appear to rapidly jump back and forth across the
>> > box boundaries, even over several nanoseconds, creating an unrealistic
>> > effect in the membrane. Is there a way to fix this visual artifact with
>> > additional options in cpptraj?
>>
>> First, just to be clear the 'autoimage' command isn't removing
>> periodic boundary conditions, it's just removing the "jumps" that
>> happen due to wrapping when PBCs are present.
>>
>> Membranes are tricky since you want the lipids "anchored", but the
>> current algorithm is really best suited to dilute systems. I added the
>> 'moveanchor' keyword for 'autoimage' specifically to try to address
>> these kinds of systems; essentially it makes the anchor the previous
>> molecule. I've had success with it for membrane systems, but you
>> should definitely test it with the problematic frames you are seeing
>> before trying it on your whole trajectory. If you still have issues
>> please try to send me off list the topology and the problematic frames
>> (or if possible the entire trajectory) and I'll see what I can do.
>>
>> Hope this helps,
>>
>> -Dan
>>
>
>
>------------------------------
>
>Message: 5
>Date: Thu, 7 Nov 2024 09:20:37 -0500
>From: Daniel Roe <daniel.r.roe.gmail.com>
>To: Enrico Martinez <jmsstarlight.gmail.com>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAAC0qObnRSYckVHHX=UYxQ7Ei6_4_U68X0QBE9W=6wFMZi-PcA.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>> One question: may I use the option 'moveanchor' with another command of ccptraj: image center familiar
>
>You're certainly welcome to try anything, but note that 'autoimage'
>and 'image' are typically mutually exclusive in that whichever command
>happens last will typically override anything the first command did.
>It might be the case sometimes that one command puts the system in a
>slightly better configuration for the second command, but the opposite
>can be true as well. So to sum up, personally I would choose one or
>the other but you're free to experiment and try anything you wish!
>
>-Dan
>
>On Thu, Nov 7, 2024 at 8:53?AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>>
>> Thank you very much Daniel !
>> I am going to test it and will report you the results ..
>> One question: may I use the option 'moveanchor' with another command of ccptraj: image center familiar
>> Sometimes it works better for membrane protein system producing the system oriented in the center of the membrane ( but still with lipid jumps)
>>
>> Enrico
>>
>> Il giorno gio 7 nov 2024 alle ore 14:23 Daniel Roe <daniel.r.roe.gmail.com> ha scritto:
>>>
>>> Hi,
>>>
>>> On Thu, Nov 7, 2024 at 3:37?AM Enrico Martinez via AMBER
>>> <amber.ambermd.org> wrote:
>>> > I still have a question about removing the periodic boundary conditions
>>> > (PBC) from membrane simulations. I used the autoimage command in cpptraj,
>>> > and it works well for keeping the protein centered in the box. However,
>>> > some lipids occasionally appear to rapidly jump back and forth across the
>>> > box boundaries, even over several nanoseconds, creating an unrealistic
>>> > effect in the membrane. Is there a way to fix this visual artifact with
>>> > additional options in cpptraj?
>>>
>>> First, just to be clear the 'autoimage' command isn't removing
>>> periodic boundary conditions, it's just removing the "jumps" that
>>> happen due to wrapping when PBCs are present.
>>>
>>> Membranes are tricky since you want the lipids "anchored", but the
>>> current algorithm is really best suited to dilute systems. I added the
>>> 'moveanchor' keyword for 'autoimage' specifically to try to address
>>> these kinds of systems; essentially it makes the anchor the previous
>>> molecule. I've had success with it for membrane systems, but you
>>> should definitely test it with the problematic frames you are seeing
>>> before trying it on your whole trajectory. If you still have issues
>>> please try to send me off list the topology and the problematic frames
>>> (or if possible the entire trajectory) and I'll see what I can do.
>>>
>>> Hope this helps,
>>>
>>> -Dan
>
>
>
>------------------------------
>
>Message: 6
>Date: Thu, 7 Nov 2024 15:33:15 +0100
>From: Enrico Martinez <jmsstarlight.gmail.com>
>To: Daniel Roe <daniel.r.roe.gmail.com>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAALQopyxUdzOehrak23jibhtyBDWaG7uTFm8+TbwO8ANAJ1+EQ.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Actually I used image as an alternative to autoimage and would like to know
>if the moveanchor option could work with it as well or if it works
>exclusively with autoimage ?
>
>Enrico
>
>
>Il giorno gio 7 nov 2024 alle ore 15:20 Daniel Roe <daniel.r.roe.gmail.com>
>ha scritto:
>
>> Hi,
>>
>> > One question: may I use the option 'moveanchor' with another command of
>> ccptraj: image center familiar
>>
>> You're certainly welcome to try anything, but note that 'autoimage'
>> and 'image' are typically mutually exclusive in that whichever command
>> happens last will typically override anything the first command did.
>> It might be the case sometimes that one command puts the system in a
>> slightly better configuration for the second command, but the opposite
>> can be true as well. So to sum up, personally I would choose one or
>> the other but you're free to experiment and try anything you wish!
>>
>> -Dan
>>
>> On Thu, Nov 7, 2024 at 8:53?AM Enrico Martinez <jmsstarlight.gmail.com>
>> wrote:
>> >
>> > Thank you very much Daniel !
>> > I am going to test it and will report you the results ..
>> > One question: may I use the option 'moveanchor' with another command of
>> ccptraj: image center familiar
>> > Sometimes it works better for membrane protein system producing the
>> system oriented in the center of the membrane ( but still with lipid jumps)
>> >
>> > Enrico
>> >
>> > Il giorno gio 7 nov 2024 alle ore 14:23 Daniel Roe <
>> daniel.r.roe.gmail.com> ha scritto:
>> >>
>> >> Hi,
>> >>
>> >> On Thu, Nov 7, 2024 at 3:37?AM Enrico Martinez via AMBER
>> >> <amber.ambermd.org> wrote:
>> >> > I still have a question about removing the periodic boundary
>> conditions
>> >> > (PBC) from membrane simulations. I used the autoimage command in
>> cpptraj,
>> >> > and it works well for keeping the protein centered in the box.
>> However,
>> >> > some lipids occasionally appear to rapidly jump back and forth across
>> the
>> >> > box boundaries, even over several nanoseconds, creating an unrealistic
>> >> > effect in the membrane. Is there a way to fix this visual artifact
>> with
>> >> > additional options in cpptraj?
>> >>
>> >> First, just to be clear the 'autoimage' command isn't removing
>> >> periodic boundary conditions, it's just removing the "jumps" that
>> >> happen due to wrapping when PBCs are present.
>> >>
>> >> Membranes are tricky since you want the lipids "anchored", but the
>> >> current algorithm is really best suited to dilute systems. I added the
>> >> 'moveanchor' keyword for 'autoimage' specifically to try to address
>> >> these kinds of systems; essentially it makes the anchor the previous
>> >> molecule. I've had success with it for membrane systems, but you
>> >> should definitely test it with the problematic frames you are seeing
>> >> before trying it on your whole trajectory. If you still have issues
>> >> please try to send me off list the topology and the problematic frames
>> >> (or if possible the entire trajectory) and I'll see what I can do.
>> >>
>> >> Hope this helps,
>> >>
>> >> -Dan
>>
>
>
>------------------------------
>
>Message: 7
>Date: Thu, 7 Nov 2024 09:56:30 -0500
>From: Daniel Roe <daniel.r.roe.gmail.com>
>To: Enrico Martinez <jmsstarlight.gmail.com>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAAC0qOZkzbi5U=sc97ApGL2Rxmrn1S+Kzr-UL1_B5XqsiSCTYw.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>?moveanchor? is only for ?autoimage?.
>
>-Dan
>
>On Thu, Nov 7, 2024 at 9:33?AM Enrico Martinez <jmsstarlight.gmail.com>
>wrote:
>
>> Actually I used image as an alternative to autoimage and would like to
>> know if the moveanchor option could work with it as well or if it works
>> exclusively with autoimage ?
>>
>> Enrico
>>
>>
>> Il giorno gio 7 nov 2024 alle ore 15:20 Daniel Roe <daniel.r.roe.gmail.com>
>> ha scritto:
>>
>>> Hi,
>>>
>>> > One question: may I use the option 'moveanchor' with another command of
>>> ccptraj: image center familiar
>>>
>>> You're certainly welcome to try anything, but note that 'autoimage'
>>> and 'image' are typically mutually exclusive in that whichever command
>>> happens last will typically override anything the first command did.
>>> It might be the case sometimes that one command puts the system in a
>>> slightly better configuration for the second command, but the opposite
>>> can be true as well. So to sum up, personally I would choose one or
>>> the other but you're free to experiment and try anything you wish!
>>>
>>> -Dan
>>>
>>> On Thu, Nov 7, 2024 at 8:53?AM Enrico Martinez <jmsstarlight.gmail.com>
>>> wrote:
>>> >
>>> > Thank you very much Daniel !
>>> > I am going to test it and will report you the results ..
>>> > One question: may I use the option 'moveanchor' with another command of
>>> ccptraj: image center familiar
>>> > Sometimes it works better for membrane protein system producing the
>>> system oriented in the center of the membrane ( but still with lipid jumps)
>>> >
>>> > Enrico
>>> >
>>> > Il giorno gio 7 nov 2024 alle ore 14:23 Daniel Roe <
>>> daniel.r.roe.gmail.com> ha scritto:
>>> >>
>>> >> Hi,
>>> >>
>>> >> On Thu, Nov 7, 2024 at 3:37?AM Enrico Martinez via AMBER
>>> >> <amber.ambermd.org> wrote:
>>> >> > I still have a question about removing the periodic boundary
>>> conditions
>>> >> > (PBC) from membrane simulations. I used the autoimage command in
>>> cpptraj,
>>> >> > and it works well for keeping the protein centered in the box.
>>> However,
>>> >> > some lipids occasionally appear to rapidly jump back and forth
>>> across the
>>> >> > box boundaries, even over several nanoseconds, creating an
>>> unrealistic
>>> >> > effect in the membrane. Is there a way to fix this visual artifact
>>> with
>>> >> > additional options in cpptraj?
>>> >>
>>> >> First, just to be clear the 'autoimage' command isn't removing
>>> >> periodic boundary conditions, it's just removing the "jumps" that
>>> >> happen due to wrapping when PBCs are present.
>>> >>
>>> >> Membranes are tricky since you want the lipids "anchored", but the
>>> >> current algorithm is really best suited to dilute systems. I added the
>>> >> 'moveanchor' keyword for 'autoimage' specifically to try to address
>>> >> these kinds of systems; essentially it makes the anchor the previous
>>> >> molecule. I've had success with it for membrane systems, but you
>>> >> should definitely test it with the problematic frames you are seeing
>>> >> before trying it on your whole trajectory. If you still have issues
>>> >> please try to send me off list the topology and the problematic frames
>>> >> (or if possible the entire trajectory) and I'll see what I can do.
>>> >>
>>> >> Hope this helps,
>>> >>
>>> >> -Dan
>>>
>>
>
>
>------------------------------
>
>Message: 8
>Date: Thu, 7 Nov 2024 16:12:20 +0100
>From: Enrico Martinez <jmsstarlight.gmail.com>
>To: Daniel Roe <daniel.r.roe.gmail.com>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAALQopy5iY4cYk=oY6GO0T5r9fLBRw_VN_Y9VV1WbpmxueR2Eg.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Okay, thank you Daniel !
>
>BTW do we have some additional option to autoimage to center the protein in
>the membrane like I could achieve with image ? If yes, would it be possible
>to combine the both options (with moveanchor) in the same autoimage command
>?
>
>Enrico
>
>Il giorno gio 7 nov 2024 alle ore 15:56 Daniel Roe <daniel.r.roe.gmail.com>
>ha scritto:
>
>> ?moveanchor? is only for ?autoimage?.
>>
>> -Dan
>>
>> On Thu, Nov 7, 2024 at 9:33?AM Enrico Martinez <jmsstarlight.gmail.com>
>> wrote:
>>
>>> Actually I used image as an alternative to autoimage and would like to
>>> know if the moveanchor option could work with it as well or if it works
>>> exclusively with autoimage ?
>>>
>>> Enrico
>>>
>>>
>>> Il giorno gio 7 nov 2024 alle ore 15:20 Daniel Roe <
>>> daniel.r.roe.gmail.com> ha scritto:
>>>
>>>> Hi,
>>>>
>>>> > One question: may I use the option 'moveanchor' with another command
>>>> of ccptraj: image center familiar
>>>>
>>>> You're certainly welcome to try anything, but note that 'autoimage'
>>>> and 'image' are typically mutually exclusive in that whichever command
>>>> happens last will typically override anything the first command did.
>>>> It might be the case sometimes that one command puts the system in a
>>>> slightly better configuration for the second command, but the opposite
>>>> can be true as well. So to sum up, personally I would choose one or
>>>> the other but you're free to experiment and try anything you wish!
>>>>
>>>> -Dan
>>>>
>>>> On Thu, Nov 7, 2024 at 8:53?AM Enrico Martinez <jmsstarlight.gmail.com>
>>>> wrote:
>>>> >
>>>> > Thank you very much Daniel !
>>>> > I am going to test it and will report you the results ..
>>>> > One question: may I use the option 'moveanchor' with another command
>>>> of ccptraj: image center familiar
>>>> > Sometimes it works better for membrane protein system producing the
>>>> system oriented in the center of the membrane ( but still with lipid jumps)
>>>> >
>>>> > Enrico
>>>> >
>>>> > Il giorno gio 7 nov 2024 alle ore 14:23 Daniel Roe <
>>>> daniel.r.roe.gmail.com> ha scritto:
>>>> >>
>>>> >> Hi,
>>>> >>
>>>> >> On Thu, Nov 7, 2024 at 3:37?AM Enrico Martinez via AMBER
>>>> >> <amber.ambermd.org> wrote:
>>>> >> > I still have a question about removing the periodic boundary
>>>> conditions
>>>> >> > (PBC) from membrane simulations. I used the autoimage command in
>>>> cpptraj,
>>>> >> > and it works well for keeping the protein centered in the box.
>>>> However,
>>>> >> > some lipids occasionally appear to rapidly jump back and forth
>>>> across the
>>>> >> > box boundaries, even over several nanoseconds, creating an
>>>> unrealistic
>>>> >> > effect in the membrane. Is there a way to fix this visual artifact
>>>> with
>>>> >> > additional options in cpptraj?
>>>> >>
>>>> >> First, just to be clear the 'autoimage' command isn't removing
>>>> >> periodic boundary conditions, it's just removing the "jumps" that
>>>> >> happen due to wrapping when PBCs are present.
>>>> >>
>>>> >> Membranes are tricky since you want the lipids "anchored", but the
>>>> >> current algorithm is really best suited to dilute systems. I added the
>>>> >> 'moveanchor' keyword for 'autoimage' specifically to try to address
>>>> >> these kinds of systems; essentially it makes the anchor the previous
>>>> >> molecule. I've had success with it for membrane systems, but you
>>>> >> should definitely test it with the problematic frames you are seeing
>>>> >> before trying it on your whole trajectory. If you still have issues
>>>> >> please try to send me off list the topology and the problematic frames
>>>> >> (or if possible the entire trajectory) and I'll see what I can do.
>>>> >>
>>>> >> Hope this helps,
>>>> >>
>>>> >> -Dan
>>>>
>>>
>
>
>------------------------------
>
>Message: 9
>Date: Thu, 7 Nov 2024 16:25:26 +0100
>From: Enrico Martinez <jmsstarlight.gmail.com>
>To: Daniel Roe <daniel.r.roe.gmail.com>
>Cc: AMBER Mailing List <amber.ambermd.org>
>Subject: Re: [AMBER] Question about cpptraj for PBC removal
>Message-ID:
> <CAALQopwJDmA-0MYeBJneZKPpxyQ3wh2CikJcVJ1ATAXcSVBjaA.mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>P.S. just testing the autoimage moveanchor I noticed that it produced a
>very chaotic lipid distribution outside the simulation box, which contained
>only protein and solvent .. ;-D
>
>Il giorno gio 7 nov 2024 alle ore 16:12 Enrico Martinez <
>jmsstarlight.gmail.com> ha scritto:
>
>> Okay, thank you Daniel !
>>
>> BTW do we have some additional option to autoimage to center the protein
>> in the membrane like I could achieve with image ? If yes, would it be
>> possible to combine the both options (with moveanchor) in the same
>> autoimage command ?
>>
>> Enrico
>>
>> Il giorno gio 7 nov 2024 alle ore 15:56 Daniel Roe <daniel.r.roe.gmail.com>
>> ha scritto:
>>
>>> ?moveanchor? is only for ?autoimage?.
>>>
>>> -Dan
>>>
>>> On Thu, Nov 7, 2024 at 9:33?AM Enrico Martinez <jmsstarlight.gmail.com>
>>> wrote:
>>>
>>>> Actually I used image as an alternative to autoimage and would like to
>>>> know if the moveanchor option could work with it as well or if it works
>>>> exclusively with autoimage ?
>>>>
>>>> Enrico
>>>>
>>>>
>>>> Il giorno gio 7 nov 2024 alle ore 15:20 Daniel Roe <
>>>> daniel.r.roe.gmail.com> ha scritto:
>>>>
>>>>> Hi,
>>>>>
>>>>> > One question: may I use the option 'moveanchor' with another command
>>>>> of ccptraj: image center familiar
>>>>>
>>>>> You're certainly welcome to try anything, but note that 'autoimage'
>>>>> and 'image' are typically mutually exclusive in that whichever command
>>>>> happens last will typically override anything the first command did.
>>>>> It might be the case sometimes that one command puts the system in a
>>>>> slightly better configuration for the second command, but the opposite
>>>>> can be true as well. So to sum up, personally I would choose one or
>>>>> the other but you're free to experiment and try anything you wish!
>>>>>
>>>>> -Dan
>>>>>
>>>>> On Thu, Nov 7, 2024 at 8:53?AM Enrico Martinez <jmsstarlight.gmail.com>
>>>>> wrote:
>>>>> >
>>>>> > Thank you very much Daniel !
>>>>> > I am going to test it and will report you the results ..
>>>>> > One question: may I use the option 'moveanchor' with another command
>>>>> of ccptraj: image center familiar
>>>>> > Sometimes it works better for membrane protein system producing the
>>>>> system oriented in the center of the membrane ( but still with lipid jumps)
>>>>> >
>>>>> > Enrico
>>>>> >
>>>>> > Il giorno gio 7 nov 2024 alle ore 14:23 Daniel Roe <
>>>>> daniel.r.roe.gmail.com> ha scritto:
>>>>> >>
>>>>> >> Hi,
>>>>> >>
>>>>> >> On Thu, Nov 7, 2024 at 3:37?AM Enrico Martinez via AMBER
>>>>> >> <amber.ambermd.org> wrote:
>>>>> >> > I still have a question about removing the periodic boundary
>>>>> conditions
>>>>> >> > (PBC) from membrane simulations. I used the autoimage command in
>>>>> cpptraj,
>>>>> >> > and it works well for keeping the protein centered in the box.
>>>>> However,
>>>>> >> > some lipids occasionally appear to rapidly jump back and forth
>>>>> across the
>>>>> >> > box boundaries, even over several nanoseconds, creating an
>>>>> unrealistic
>>>>> >> > effect in the membrane. Is there a way to fix this visual artifact
>>>>> with
>>>>> >> > additional options in cpptraj?
>>>>> >>
>>>>> >> First, just to be clear the 'autoimage' command isn't removing
>>>>> >> periodic boundary conditions, it's just removing the "jumps" that
>>>>> >> happen due to wrapping when PBCs are present.
>>>>> >>
>>>>> >> Membranes are tricky since you want the lipids "anchored", but the
>>>>> >> current algorithm is really best suited to dilute systems. I added
>>>>> the
>>>>> >> 'moveanchor' keyword for 'autoimage' specifically to try to address
>>>>> >> these kinds of systems; essentially it makes the anchor the previous
>>>>> >> molecule. I've had success with it for membrane systems, but you
>>>>> >> should definitely test it with the problematic frames you are seeing
>>>>> >> before trying it on your whole trajectory. If you still have issues
>>>>> >> please try to send me off list the topology and the problematic
>>>>> frames
>>>>> >> (or if possible the entire trajectory) and I'll see what I can do.
>>>>> >>
>>>>> >> Hope this helps,
>>>>> >>
>>>>> >> -Dan
>>>>>
>>>>
>
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Received on Thu Nov 07 2024 - 18:00:02 PST
