VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Mon Feb 05 2024 - 19:33:47 CST

Thanks!

I also see that -is was replaced with -sc. This means we now specify the
actual concentration of ions, no longer the total concentration "defined
as (#Na+#Cl)/V" as in the past. So, if you have 150 mM of NaCl you specify
"-sc 0.15" instead of "-is 0.3" as in the past, right?

Thanks!

      Gianluca

On Tue, 6 Feb 2024, Vermaas, Josh wrote:

> Yeah. CUDA without ray tracing should be fine.
>
> -Josh
>
> On 2/5/24, 4:31 PM, "Gianluca Interlandi" <gianluca_at_u.washington.edu <mailto:gianluca_at_u.washington.edu>> wrote:
>
>
> I just downloaded the version without "RTX RTRT". That should be enough,
> right? Since I don't have a video card capable of "RTX RTRT" (with at
> least 6 GB).
>
>
> Gianluca
>
>
> On Mon, 5 Feb 2024, Josh wrote:
>
>
>> Hi Gianluca,
>>
>> You will be much happier if you install VMD 1.9.4a57. I know it says alpha,
>> and alpha's can be scary, but that is probably the easiest path forward.
>> Since the *normal* way you'd get the differences is to make a diff between
>> the sources, which is probably more work than you want.
>>
>> -Josh
>>
>> On 2/5/24 1:58 PM, Gianluca Interlandi wrote:
>>> Dear all,
>>>
>>> I have been using an older version of VMD and I am now looking at version
>>> 1.9.3. I see that the ParseFEP plugin in VMD 1.9.3 can be run from the
>>> command line. When I launch it, it says: "ParseFEP: Version 1.9.2". I see
>>> though that the latest version of ParseFEP is 2.0. Is there a place where I
>>> can read about the differences between versions 1.9.2 and 2.0 and also
>>> download version 2.0?
>>>
>>> My other question is about the plugins solvate and autoionize. In the past
>>> (like in 1.8.7) they were not able to produce a PSF with extended atom
>>> types such as for glycans or CGenFF. I know that this was solved at some
>>> point. Is this already the case for 1.9.3? (Just confirming)
>>>
>>> I would appreciate any help on this.
>>>
>>> Thanks!
>>>
>>> Gianluca
>>>
>>> -----------------------------------------------------
>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu <mailto:gianluca_at_u.washington.edu>
>>> +1 (206) 685 4435
>>> https://urldefense.com/v3/__http://gianluca.today/__;!!DZ3fjg!_kpSy3gBQ_AMVrDhJTIx1IgDvuJfXKjzTDcNAlAmMYxIZ5ZHF9Z2-5hIU_1_NlzxZYQpdyKpYy7UX1_0pl01ZpThPTA$ <https://urldefense.com/v3/__http://gianluca.today/__;!!DZ3fjg!_kpSy3gBQ_AMVrDhJTIx1IgDvuJfXKjzTDcNAlAmMYxIZ5ZHF9Z2-5hIU_1_NlzxZYQpdyKpYy7UX1_0pl01ZpThPTA$>
>>> Department of Bioengineering
>>> University of Washington, Seattle WA U.S.A.
>>> -----------------------------------------------------
>>>
>>
>> --
>> Josh Vermaas
>>
>> vermaasj_at_msu.edu <mailto:vermaasj_at_msu.edu>
>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular
>> Biology
>> Michigan State University
>> vermaaslab.github.io
>>
>>
>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu <mailto:gianluca_at_u.washington.edu>
> +1 (206) 685 4435
> https://urldefense.com/v3/__http://gianluca.today/__;!!HXCxUKc!0MzZtncFJArXuapzA7z8IFkLvznGrZIa-_1_5nCS1TCdis2jT9tajPx8UXOF8glgD4xHSxdwO_0XxmK9_TWXERMg$ <https://urldefense.com/v3/__http://gianluca.today/__;!!HXCxUKc!0MzZtncFJArXuapzA7z8IFkLvznGrZIa-_1_5nCS1TCdis2jT9tajPx8UXOF8glgD4xHSxdwO_0XxmK9_TWXERMg$>
>
>
> Department of Bioengineering
> University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     https://urldefense.com/v3/__http://gianluca.today/__;!!DZ3fjg!-_PfwSLRaVxrTFH2AnFLyhCPMckXnnMtURogkaoPWV0-dFxI1t8QX1aye8GhhIroIcwu7iDkyJtGieDnFg037901QJc$

Department of Bioengineering
University of Washington, Seattle WA U.S.A.
-----------------------------------------------------